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install required packages

install.packages("geepack",repos="http://cran.us.r-project.org")
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages(c("lme4","mi","MASS"),repos="http://cran.us.r-project.org")
## Installing packages into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("unbalanced",repos="http://cran.us.r-project.org") 
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("crossval",repos="http://cran.us.r-project.org") 
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("ada",repos="http://cran.us.r-project.org")
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("e1071",repos="http://cran.us.r-project.org")
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("rpart",repos="http://cran.us.r-project.org")
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("class",repos="http://cran.us.r-project.org")
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages(c("RWeka","rJava"),repos="http://cran.us.r-project.org")
## Installing packages into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
##   There is a binary version available but the source version is
##   later:
##       binary source needs_compilation
## RWeka 0.4-26 0.4-29             FALSE
## 
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
## installing the source package 'RWeka'
install.packages("lme4",repos="http://cran.us.r-project.org") 
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("geepack",repos="http://cran.us.r-project.org") 
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("mi",repos="http://cran.us.r-project.org") 
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
install.packages("unbalanced",repos="http://cran.us.r-project.org") 
## Installing package into '/Users/MingT/Library/R/3.3/library'
## (as 'lib' is unspecified)
## 
## The downloaded binary packages are in
##  /var/folders/s8/0_mb4tr92mlfhspqc783k8z80000gn/T//RtmpwzaaGc/downloaded_packages
options(warn=-1) 
####data manipulation #######
setwd("~/documents/PPMI") #set working director
clinical<-read.csv("ppmi_clinical.csv",header=TRUE) #read raw data
colnames(clinical)[2]<-"FID_IID" 
ppmi_new<-read.csv("PPMI_GSA_clinical.csv",header=TRUE)
merged_dataset<-merge(ppmi_new,clinical,by="FID_IID",all.x=TRUE) #merge clinical data with brain image
write.csv(merged_dataset,"ppmi_clinical_complete.csv")
ppmi<-merged_dataset[,c(1:399,820:823,833,832,816)] #Select "tier 1" UPDRSs
head(ppmi)
##   FID_IID X.x L_insular_cortex_AvgMeanCurvature
## 1    3000   1                        0.10339303
## 2    3001   2                        0.11044503
## 3    3002   3                        0.10091019
## 4    3003   4                        0.09726433
## 5    3004   5                        0.10955031
## 6    3006   6                        0.09733524
##   L_insular_cortex_ComputeArea L_insular_cortex_Volume
## 1                     2763.365                8779.951
## 2                     2917.938                8754.107
## 3                     2505.515                8089.185
## 4                     3284.796               11446.049
## 5                     2802.992                9000.509
## 6                     3188.515               11004.131
##   L_insular_cortex_ShapeIndex L_insular_cortex_Curvedness
## 1                   0.3192754                   0.1094209
## 2                   0.3207401                   0.1033839
## 3                   0.3191578                   0.1099705
## 4                   0.3150762                   0.0991298
## 5                   0.3272781                   0.1144485
## 6                   0.3040458                   0.1091740
##   R_insular_cortex_AvgMeanCurvature R_insular_cortex_ComputeArea
## 1                         0.1159638                     2291.633
## 2                         0.1160668                     2342.961
## 3                         0.1077885                     2073.981
## 4                         0.1014219                     2320.993
## 5                         0.1126108                     2225.154
## 6                         0.1086814                     2135.745
##   R_insular_cortex_Volume R_insular_cortex_ShapeIndex
## 1                5482.136                   0.2664319
## 2                5732.367                   0.3149570
## 3                5321.370                   0.2709259
## 4                6395.721                   0.3003472
## 5                5567.333                   0.3058957
## 6                5583.177                   0.3187932
##   R_insular_cortex_Curvedness L_cingulate_gyrus_AvgMeanCurvature
## 1                   0.1292846                          0.1332509
## 2                   0.1215921                          0.1246343
## 3                   0.1345651                          0.1355602
## 4                   0.1126387                          0.1236226
## 5                   0.1315195                          0.1274116
## 6                   0.1205962                          0.1298253
##   L_cingulate_gyrus_ComputeArea L_cingulate_gyrus_Volume
## 1                      3477.519                 8072.617
## 2                      4381.930                11205.127
## 3                      3221.540                 7439.645
## 4                      4658.949                12443.624
## 5                      4016.731                 9922.555
## 6                      4188.552                10502.193
##   L_cingulate_gyrus_ShapeIndex L_cingulate_gyrus_Curvedness
## 1                    0.4406856                   0.08024956
## 2                    0.4349292                   0.06714417
## 3                    0.4396813                   0.08652417
## 4                    0.4556403                   0.06749613
## 5                    0.4316057                   0.07150800
## 6                    0.4510032                   0.07495887
##   R_cingulate_gyrus_AvgMeanCurvature R_cingulate_gyrus_ComputeArea
## 1                          0.1319288                      4131.343
## 2                          0.1249111                      4610.447
## 3                          0.1458248                      3194.348
## 4                          0.1361298                      4028.330
## 5                          0.1288771                      3918.263
## 6                          0.1277486                      4352.117
##   R_cingulate_gyrus_Volume R_cingulate_gyrus_ShapeIndex
## 1                10526.958                    0.4419433
## 2                12246.549                    0.4350192
## 3                 7264.683                    0.4268223
## 4                 9681.935                    0.4498362
## 5                10227.022                    0.4462917
## 6                11528.466                    0.4498547
##   R_cingulate_gyrus_Curvedness L_caudate_AvgMeanCurvature
## 1                   0.08182803                  0.2011498
## 2                   0.07081687                  0.2392929
## 3                   0.09480283                  0.1833535
## 4                   0.08071711                  0.1983211
## 5                   0.07295120                  0.1958644
## 6                   0.07407571                  0.2115839
##   L_caudate_ComputeArea L_caudate_Volume L_caudate_ShapeIndex
## 1              801.8746        1207.2003            0.2811706
## 2              621.5344         821.8991            0.2473931
## 3              876.9414        1364.8601            0.2580652
## 4             1019.6664        1570.3055            0.3164872
## 5             1086.9388        1772.9241            0.2960296
## 6              863.4775        1341.3073            0.2780000
##   L_caudate_Curvedness R_caudate_AvgMeanCurvature R_caudate_ComputeArea
## 1            0.2364463                  0.1884890              999.3843
## 2            0.3429220                  0.1558452             1302.1458
## 3            0.2308683                  0.1763202             1056.2200
## 4            0.1760060                  0.1703131             1208.7987
## 5            0.1854576                  0.1739900             1267.7040
## 6            0.2513109                  0.1441599             1247.1482
##   R_caudate_Volume R_caudate_ShapeIndex R_caudate_Curvedness
## 1         1698.516            0.2611800            0.1978461
## 2         2526.248            0.2892424            0.1496714
## 3         1965.206            0.2970232            0.1854200
## 4         2268.701            0.2912487            0.1568764
## 5         2262.694            0.3027961            0.1599818
## 6         2678.534            0.3008528            0.1360011
##   L_putamen_AvgMeanCurvature L_putamen_ComputeArea L_putamen_Volume
## 1                  0.1623982              1261.750         2595.533
## 2                  0.2022735              1029.175         1543.017
## 3                  0.1418179              1275.905         2696.695
## 4                  0.1409578              1482.684         3046.274
## 5                  0.1814492              1050.227         2028.140
## 6                  0.1787384              1229.513         2482.513
##   L_putamen_ShapeIndex L_putamen_Curvedness R_putamen_AvgMeanCurvature
## 1            0.2857386            0.1766909                  0.1209783
## 2            0.2853486            0.2320214                  0.1111208
## 3            0.2876249            0.1566615                  0.1446244
## 4            0.3041529            0.1523438                  0.1402802
## 5            0.2769987            0.1868594                  0.1214390
## 6            0.2923973            0.2064697                  0.1628602
##   R_putamen_ComputeArea R_putamen_Volume R_putamen_ShapeIndex
## 1              1471.391         3429.283            0.2861552
## 2              1680.197         3792.201            0.2670927
## 3              1375.725         2966.682            0.2936447
## 4              1310.875         2755.439            0.2913030
## 5              1511.374         3458.706            0.2978874
## 6              1298.760         2595.811            0.3136044
##   R_putamen_Curvedness L_hippocampus_AvgMeanCurvature
## 1            0.1400700                      0.1332656
## 2            0.1332011                      0.1226265
## 3            0.1546469                      0.1304512
## 4            0.1606766                      0.1191435
## 5            0.1362302                      0.1242598
## 6            0.1666391                      0.1116450
##   L_hippocampus_ComputeArea L_hippocampus_Volume L_hippocampus_ShapeIndex
## 1                  1456.701             3441.663                0.3149792
## 2                  1769.672             4737.038                0.3201427
## 3                  1529.759             3736.040                0.3189372
## 4                  1679.536             4458.264                0.3512617
## 5                  1552.218             3718.433                0.2814200
## 6                  1878.617             5078.684                0.3338252
##   L_hippocampus_Curvedness R_hippocampus_AvgMeanCurvature
## 1                0.1491479                      0.1150244
## 2                0.1179703                      0.1312485
## 3                0.1239492                      0.1179286
## 4                0.1092478                      0.1174198
## 5                0.1435228                      0.1158403
## 6                0.1089977                      0.1140703
##   R_hippocampus_ComputeArea R_hippocampus_Volume R_hippocampus_ShapeIndex
## 1                  1825.942             4843.637                0.3148975
## 2                  1578.946             3817.621                0.2894075
## 3                  1799.438             4665.167                0.3102413
## 4                  1850.187             5177.618                0.3050725
## 5                  1762.969             4529.123                0.3331539
## 6                  1976.793             5508.145                0.3469782
##   R_hippocampus_Curvedness cerebellum_AvgMeanCurvature
## 1               0.11740466                  0.11124426
## 2               0.14824928                 -0.01081359
## 3               0.12306355                  2.66084380
## 4               0.12038557                  0.03830412
## 5               0.12558195                  0.07386941
## 6               0.09903943                 -0.15067070
##   cerebellum_ComputeArea cerebellum_Volume cerebellum_ShapeIndex
## 1               17233.65          148735.2             0.3834653
## 2               20909.58          185742.6             0.2932517
## 3               17627.01          155632.3             0.3074467
## 4               15506.38          133878.8             0.3423785
## 5               17130.48          141371.6             0.4104847
## 6               17778.92          155220.7             0.3737010
##   cerebellum_Curvedness brainstem_AvgMeanCurvature brainstem_ComputeArea
## 1            0.06011980                 0.06972784              6394.451
## 2            0.16746150                 0.06346277              7741.742
## 3           34.49791700                 0.07059487              6456.809
## 4            0.11113414                 0.06736263              6987.226
## 5            0.04983775                 0.06649145              6979.882
## 6            2.31151870                 0.07263206              7253.218
##   brainstem_Volume brainstem_ShapeIndex brainstem_Curvedness
## 1         35754.04            0.3087066           0.07605392
## 2         45610.19            0.3192699           0.07574226
## 3         35781.50            0.2843547           0.08571674
## 4         41214.97            0.3308024           0.07034704
## 5         40971.91            0.3150985           0.07551081
## 6         43166.55            0.3444916           0.06780533
##   L_superior_frontal_gyrus_AvgMeanCurvature
## 1                                0.08100099
## 2                                0.07951369
## 3                                0.07711980
## 4                                0.07734055
## 5                                0.07925338
## 6                                0.07307774
##   L_superior_frontal_gyrus_ComputeArea L_superior_frontal_gyrus_Volume
## 1                            10323.433                        48405.02
## 2                            11363.699                        53308.55
## 3                             9510.621                        43467.55
## 4                            11380.541                        53081.02
## 5                            10844.077                        54149.27
## 6                            11352.045                        57213.15
##   L_superior_frontal_gyrus_ShapeIndex L_superior_frontal_gyrus_Curvedness
## 1                           0.3776485                          0.05680316
## 2                           0.3744766                          0.05133303
## 3                           0.3782946                          0.05615867
## 4                           0.3537120                          0.05340476
## 5                           0.3517075                          0.05468875
## 6                           0.3776325                          0.05042987
##   R_superior_frontal_gyrus_AvgMeanCurvature
## 1                                0.09402456
## 2                                0.08691916
## 3                                0.08439535
## 4                                0.08471537
## 5                                0.07839364
## 6                                0.08651596
##   R_superior_frontal_gyrus_ComputeArea R_superior_frontal_gyrus_Volume
## 1                            10022.785                        46506.77
## 2                            11134.168                        52396.24
## 3                             9314.438                        40798.21
## 4                            12392.188                        63075.63
## 5                            10432.360                        50157.89
## 6                            11086.727                        54957.84
##   R_superior_frontal_gyrus_ShapeIndex R_superior_frontal_gyrus_Curvedness
## 1                           0.4016202                          0.05349894
## 2                           0.4484875                          0.04586595
## 3                           0.3865799                          0.05608831
## 4                           0.3838962                          0.05540523
## 5                           0.3818891                          0.04603138
## 6                           0.3856457                          0.05724273
##   L_middle_frontal_gyrus_AvgMeanCurvature
## 1                              0.07402717
## 2                              0.11952615
## 3                              0.16637044
## 4                              0.07611775
## 5                              0.08236869
## 6                              0.07264456
##   L_middle_frontal_gyrus_ComputeArea L_middle_frontal_gyrus_Volume
## 1                           9105.836                      48109.75
## 2                           9988.897                      52452.81
## 3                           8710.422                      46543.30
## 4                           9334.861                      50114.31
## 5                           8877.312                      47018.99
## 6                           9751.798                      53668.02
##   L_middle_frontal_gyrus_ShapeIndex L_middle_frontal_gyrus_Curvedness
## 1                         0.3078132                        0.07945989
## 2                         0.3481521                        0.06595413
## 3                         0.3184140                        0.08178205
## 4                         0.3379107                        0.05968499
## 5                         0.3329076                        0.06226124
## 6                         0.2952311                        0.71030190
##   R_middle_frontal_gyrus_AvgMeanCurvature
## 1                              0.07499459
## 2                              0.07785072
## 3                              0.07515226
## 4                              0.07302976
## 5                              0.08970708
## 6                              0.07306901
##   R_middle_frontal_gyrus_ComputeArea R_middle_frontal_gyrus_Volume
## 1                           8851.557                      49372.76
## 2                           9660.306                      54012.12
## 3                           7882.520                      42838.83
## 4                           9610.101                      55047.20
## 5                           8067.214                      43606.92
## 6                           9913.557                      57678.77
##   R_middle_frontal_gyrus_ShapeIndex R_middle_frontal_gyrus_Curvedness
## 1                         0.2965402                        0.06233485
## 2                         0.3178475                        0.05932451
## 3                         0.3149322                        0.06536620
## 4                         0.3090931                        0.05702957
## 5                         0.2863362                        0.06827832
## 6                         0.3256466                        0.05722431
##   L_inferior_frontal_gyrus_AvgMeanCurvature
## 1                                0.09232418
## 2                                0.08264828
## 3                                0.09041177
## 4                                0.08631535
## 5                                0.08764468
## 6                                0.07900866
##   L_inferior_frontal_gyrus_ComputeArea L_inferior_frontal_gyrus_Volume
## 1                             4781.623                        21839.74
## 2                             5091.727                        25113.25
## 3                             4106.199                        17136.94
## 4                             4556.781                        20029.15
## 5                             3760.532                        15548.01
## 6                             5508.372                        27544.42
##   L_inferior_frontal_gyrus_ShapeIndex L_inferior_frontal_gyrus_Curvedness
## 1                           0.3050616                          0.09872059
## 2                           0.3067739                          0.09213249
## 3                           0.2913024                          0.11054313
## 4                           0.3102240                          0.09227259
## 5                           0.2875925                          0.10289127
## 6                           0.3188633                          0.07897555
##   R_inferior_frontal_gyrus_AvgMeanCurvature
## 1                                0.08158166
## 2                                0.07610716
## 3                                0.08009501
## 4                                0.08504603
## 5                                0.08159838
## 6                                0.07464060
##   R_inferior_frontal_gyrus_ComputeArea R_inferior_frontal_gyrus_Volume
## 1                             4948.708                        24562.58
## 2                             5612.835                        28546.87
## 3                             4664.688                        22296.34
## 4                             4665.766                        21012.86
## 5                             4851.100                        23619.47
## 6                             5576.678                        28124.61
##   R_inferior_frontal_gyrus_ShapeIndex R_inferior_frontal_gyrus_Curvedness
## 1                           0.3293004                          0.07844599
## 2                           0.3206594                          0.06914873
## 3                           0.3192303                          0.08402686
## 4                           0.2894400                          0.09034790
## 5                           0.3095379                          0.08705973
## 6                           0.3361318                          0.07954666
##   L_precentral_gyrus_AvgMeanCurvature L_precentral_gyrus_ComputeArea
## 1                          0.08822059                       5945.166
## 2                          0.09409574                       6634.533
## 3                          0.06789780                       5764.879
## 4                          0.08122137                       6430.497
## 5                          0.08871625                       6380.224
## 6                          0.09053335                       6095.706
##   L_precentral_gyrus_Volume L_precentral_gyrus_ShapeIndex
## 1                  22275.78                     0.3413521
## 2                  25205.30                     0.3518310
## 3                  20273.68                     0.3225783
## 4                  24588.46                     0.3580851
## 5                  24206.99                     0.3314704
## 6                  21866.00                     0.3506974
##   L_precentral_gyrus_Curvedness R_precentral_gyrus_AvgMeanCurvature
## 1                    0.09154550                          0.08797655
## 2                    0.09609143                          0.08857492
## 3                    0.10622379                          0.09876766
## 4                    0.08148415                          0.08939573
## 5                    0.08331495                          0.09300800
## 6                    0.07997279                          0.08878694
##   R_precentral_gyrus_ComputeArea R_precentral_gyrus_Volume
## 1                       5820.268                  23036.32
## 2                       6057.209                  23691.55
## 3                       5726.844                  21134.83
## 4                       5780.951                  21180.83
## 5                       6269.956                  25722.87
## 6                       5792.416                  21327.76
##   R_precentral_gyrus_ShapeIndex R_precentral_gyrus_Curvedness
## 1                     0.3609946                    0.07470327
## 2                     0.3654834                    0.07582953
## 3                     0.3747464                    0.07726095
## 4                     0.3623383                    0.07459419
## 5                     0.3483505                    0.08644210
## 6                     0.3695930                    0.07515290
##   L_middle_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                    0.10756427
## 2                                    0.09504461
## 3                                    0.11195838
## 4                                    0.10857720
## 5                                    0.09857074
## 6                                    0.09876597
##   L_middle_orbitofrontal_gyrus_ComputeArea
## 1                                 2959.834
## 2                                 3190.647
## 3                                 2643.407
## 4                                 2947.184
## 5                                 3115.858
## 6                                 2895.487
##   L_middle_orbitofrontal_gyrus_Volume
## 1                            8567.099
## 2                           10459.919
## 3                            7667.457
## 4                            8872.217
## 5                            9984.053
## 6                            8819.313
##   L_middle_orbitofrontal_gyrus_ShapeIndex
## 1                               0.2946531
## 2                               0.2909523
## 3                               0.2836412
## 4                               0.2768023
## 5                               0.3300948
## 6                               0.2772049
##   L_middle_orbitofrontal_gyrus_Curvedness
## 1                              0.09477899
## 2                              0.08821871
## 3                              0.10691605
## 4                              0.08969987
## 5                              0.07829051
## 6                              0.09271120
##   R_middle_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                     0.1192333
## 2                                     0.1093085
## 3                                     0.1086538
## 4                                     0.1020976
## 5                                     0.1122697
## 6                                     0.1085550
##   R_middle_orbitofrontal_gyrus_ComputeArea
## 1                                 3188.606
## 2                                 3108.103
## 3                                 2871.688
## 4                                 3382.121
## 5                                 3031.104
## 6                                 3071.431
##   R_middle_orbitofrontal_gyrus_Volume
## 1                            9229.549
## 2                            9611.130
## 3                            8529.517
## 4                           10460.593
## 5                            8912.429
## 6                            9319.833
##   R_middle_orbitofrontal_gyrus_ShapeIndex
## 1                               0.2755525
## 2                               0.3060040
## 3                               0.2800826
## 4                               0.2821486
## 5                               0.3010434
## 6                               0.2772180
##   R_middle_orbitofrontal_gyrus_Curvedness
## 1                              0.09481500
## 2                              0.09612964
## 3                              0.09927428
## 4                              0.09002830
## 5                              0.10531771
## 6                              0.09974456
##   L_lateral_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                      0.1272921
## 2                                      0.1274801
## 3                                      0.1294754
## 4                                      0.1348371
## 5                                      0.1336065
## 6                                      0.1441287
##   L_lateral_orbitofrontal_gyrus_ComputeArea
## 1                                  1953.602
## 2                                  1940.454
## 3                                  1705.715
## 4                                  1891.861
## 5                                  1771.899
## 6                                  2158.262
##   L_lateral_orbitofrontal_gyrus_Volume
## 1                             4038.399
## 2                             4320.333
## 3                             3392.857
## 4                             4326.737
## 5                             3627.903
## 6                             4168.530
##   L_lateral_orbitofrontal_gyrus_ShapeIndex
## 1                                0.2902372
## 2                                0.2895921
## 3                                0.2407804
## 4                                0.3053100
## 5                                0.3058705
## 6                                0.2848462
##   L_lateral_orbitofrontal_gyrus_Curvedness
## 1                                0.1766418
## 2                                0.1775847
## 3                                0.1863002
## 4                                0.1467295
## 5                                0.1678090
## 6                                0.1479501
##   R_lateral_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                      0.1309167
## 2                                      0.1397253
## 3                                      0.1562820
## 4                                      0.1467773
## 5                                      0.1434309
## 6                                      0.1299206
##   R_lateral_orbitofrontal_gyrus_ComputeArea
## 1                                  1705.245
## 2                                  1953.675
## 3                                  1889.294
## 4                                  1708.332
## 5                                  1831.184
## 6                                  1982.338
##   R_lateral_orbitofrontal_gyrus_Volume
## 1                             3655.639
## 2                             4093.492
## 3                             3713.498
## 4                             3450.264
## 5                             3699.269
## 6                             4330.369
##   R_lateral_orbitofrontal_gyrus_ShapeIndex
## 1                                0.2628306
## 2                                0.2971379
## 3                                0.2971216
## 4                                0.2777466
## 5                                0.2543070
## 6                                0.2892046
##   R_lateral_orbitofrontal_gyrus_Curvedness L_gyrus_rectus_AvgMeanCurvature
## 1                                0.1874613                       0.1964838
## 2                                0.1634671                       0.2078852
## 3                                0.1559738                       0.2408347
## 4                                0.1939476                       0.1516295
## 5                                0.1342819                       0.2300583
## 6                                0.1474630                       0.2162944
##   L_gyrus_rectus_ComputeArea L_gyrus_rectus_Volume
## 1                   980.4423             1619.7333
## 2                  1143.0779             1785.8225
## 3                   690.5019              974.7885
## 4                  1360.0150             2701.2750
## 5                   972.7225             1495.7976
## 6                   908.7805             1437.0935
##   L_gyrus_rectus_ShapeIndex L_gyrus_rectus_Curvedness
## 1                 0.2539865                 0.2170866
## 2                 0.2893511                 0.2222131
## 3                 0.2537049                 0.3158460
## 4                 0.2726588                 0.1739792
## 5                 0.2888985                 0.2187143
## 6                 0.2653972                 0.2614590
##   R_gyrus_rectus_AvgMeanCurvature R_gyrus_rectus_ComputeArea
## 1                       0.1471301                   1411.747
## 2                       0.1519435                   1408.899
## 3                       0.1727085                   1099.657
## 4                       0.1333407                   1501.545
## 5                       0.1937611                   1171.779
## 6                       0.1778007                   1229.734
##   R_gyrus_rectus_Volume R_gyrus_rectus_ShapeIndex
## 1              2781.022                 0.2794396
## 2              2763.942                 0.2612030
## 3              1962.041                 0.2749456
## 4              3253.902                 0.2725946
## 5              1957.030                 0.2926626
## 6              2222.924                 0.2696461
##   R_gyrus_rectus_Curvedness L_postcentral_gyrus_AvgMeanCurvature
## 1                 0.1832981                           0.10508093
## 2                 0.1959469                           0.09087086
## 3                 0.1815064                           0.10574263
## 4                 0.1462237                           0.09284356
## 5                 0.2194676                           0.11175828
## 6                 0.1897803                           0.09467665
##   L_postcentral_gyrus_ComputeArea L_postcentral_gyrus_Volume
## 1                        5852.116                   21565.38
## 2                        5952.575                   22426.55
## 3                        6141.619                   22325.22
## 4                        5269.063                   17683.91
## 5                        6435.081                   22275.72
## 6                        5747.097                   19637.25
##   L_postcentral_gyrus_ShapeIndex L_postcentral_gyrus_Curvedness
## 1                      0.3432217                     0.09591017
## 2                      0.3305127                     0.08240747
## 3                      0.3112023                     0.08712497
## 4                      0.3287937                     0.09031591
## 5                      0.3179572                     0.10079832
## 6                      0.3216686                     0.07746661
##   R_postcentral_gyrus_AvgMeanCurvature R_postcentral_gyrus_ComputeArea
## 1                           0.09829028                        5843.220
## 2                           0.07717761                        6274.401
## 3                           0.08963424                        5729.988
## 4                           0.44033816                        6292.385
## 5                           0.10047813                        7229.333
## 6                           0.09394788                        5858.971
##   R_postcentral_gyrus_Volume R_postcentral_gyrus_ShapeIndex
## 1                   21663.67                      0.3266972
## 2                   26116.10                      0.3320086
## 3                   18710.21                      0.3128947
## 4                   25337.88                      0.3112892
## 5                   30405.49                      0.2807297
## 6                   20709.22                      0.3246994
##   R_postcentral_gyrus_Curvedness
## 1                     0.09283601
## 2                     0.08080232
## 3                     0.08389504
## 4                     0.09159105
## 5                     0.09136557
## 6                     0.07954769
##   L_superior_parietal_gyrus_AvgMeanCurvature
## 1                                 0.10138974
## 2                                 0.15642601
## 3                                 0.07739609
## 4                                 0.08403327
## 5                                 0.08048810
## 6                                 0.08444352
##   L_superior_parietal_gyrus_ComputeArea L_superior_parietal_gyrus_Volume
## 1                              5358.074                         25996.28
## 2                              5228.112                         22835.86
## 3                              4866.638                         22815.78
## 4                              4257.462                         17449.40
## 5                              5282.335                         23962.46
## 6                              5567.526                         25985.85
##   L_superior_parietal_gyrus_ShapeIndex
## 1                            0.2905781
## 2                            0.3180919
## 3                            0.2827858
## 4                            0.2894923
## 5                            0.2729865
## 6                            0.2984420
##   L_superior_parietal_gyrus_Curvedness
## 1                           0.09668629
## 2                           0.08668642
## 3                           0.09646292
## 4                           0.09863686
## 5                           0.09134870
## 6                           0.08186932
##   R_superior_parietal_gyrus_AvgMeanCurvature
## 1                                 0.08267691
## 2                                 0.07807680
## 3                                 0.07335306
## 4                                 0.08272585
## 5                                 0.08455538
## 6                                 0.07725251
##   R_superior_parietal_gyrus_ComputeArea R_superior_parietal_gyrus_Volume
## 1                              5673.109                         28109.21
## 2                              5121.035                         25387.02
## 3                              5449.289                         28970.75
## 4                              4690.151                         20883.88
## 5                              5704.847                         28112.53
## 6                              5932.755                         30813.30
##   R_superior_parietal_gyrus_ShapeIndex
## 1                            0.2624184
## 2                            0.2799022
## 3                            0.2819246
## 4                            0.2475126
## 5                            0.2767437
## 6                            0.2791106
##   R_superior_parietal_gyrus_Curvedness
## 1                           0.08636291
## 2                           0.08711799
## 3                           0.08845111
## 4                           0.09899254
## 5                           0.09276057
## 6                           0.09179036
##   L_supramarginal_gyrus_AvgMeanCurvature L_supramarginal_gyrus_ComputeArea
## 1                             0.10292991                          3257.416
## 2                             0.08960319                          3766.590
## 3                             0.09134826                          3766.664
## 4                             0.09775341                          3466.433
## 5                             0.10188387                          3980.114
## 6                             0.08835363                          3835.389
##   L_supramarginal_gyrus_Volume L_supramarginal_gyrus_ShapeIndex
## 1                     12039.86                        0.2978995
## 2                     14904.22                        0.3068543
## 3                     15181.61                        0.2855105
## 4                     13164.55                        0.3096961
## 5                     16108.37                        0.3027252
## 6                     15204.89                        0.2790939
##   L_supramarginal_gyrus_Curvedness R_supramarginal_gyrus_AvgMeanCurvature
## 1                       0.10960597                             0.09751207
## 2                       0.09030263                             0.09359056
## 3                       0.10938548                             0.10048632
## 4                       0.10245745                             0.06148638
## 5                       0.09792726                             0.08745759
## 6                       0.10536623                             0.09508114
##   R_supramarginal_gyrus_ComputeArea R_supramarginal_gyrus_Volume
## 1                          2875.999                    11212.458
## 2                          2943.982                    11236.216
## 3                          2397.780                     8306.699
## 4                          2804.045                     8747.607
## 5                          3323.411                    11621.903
## 6                          3334.477                    12910.579
##   R_supramarginal_gyrus_ShapeIndex R_supramarginal_gyrus_Curvedness
## 1                        0.2874430                        0.1262914
## 2                        0.3043556                        0.1132410
## 3                        0.2951722                        0.1185719
## 4                        0.2294821                        0.1899408
## 5                        0.2680114                        0.1379686
## 6                        0.2954146                        0.1125512
##   L_angular_gyrus_AvgMeanCurvature L_angular_gyrus_ComputeArea
## 1                       0.09211609                    3518.132
## 2                       0.08332833                    4499.945
## 3                       0.08921783                    3811.192
## 4                       0.07404549                    3802.423
## 5                       0.08713398                    4175.902
## 6                       0.08054429                    4541.701
##   L_angular_gyrus_Volume L_angular_gyrus_ShapeIndex
## 1               13911.83                  0.2931503
## 2               18707.85                  0.3069968
## 3               15449.27                  0.2856840
## 4               15203.80                  0.3085006
## 5               16791.69                  0.2809210
## 6               20320.15                  0.2977993
##   L_angular_gyrus_Curvedness R_angular_gyrus_AvgMeanCurvature
## 1                 0.12313346                       0.08108542
## 2                 0.08690669                       0.10242639
## 3                 0.10374778                       0.08759734
## 4                 0.12590794                       0.09118984
## 5                 0.10382951                       0.07759675
## 6                 0.09659023                       0.09858398
##   R_angular_gyrus_ComputeArea R_angular_gyrus_Volume
## 1                    3752.691               13254.46
## 2                    3666.847               13003.38
## 3                    3912.730               15305.92
## 4                    4120.223               16804.60
## 5                    3788.444               12779.83
## 6                    4638.663               17428.22
##   R_angular_gyrus_ShapeIndex R_angular_gyrus_Curvedness
## 1                  0.2942332                 0.11413383
## 2                  0.2994884                 0.11061017
## 3                  0.2862641                 0.11115348
## 4                  0.3036556                 0.09627947
## 5                  0.2554384                 0.14470702
## 6                  0.2893637                 0.09096058
##   L_precuneus_AvgMeanCurvature L_precuneus_ComputeArea L_precuneus_Volume
## 1                   0.09815007                3352.910          10894.338
## 2                   0.10264540                3065.234           9302.229
## 3                   0.10856181                2888.769           8250.564
## 4                   0.10954109                3356.718          10437.275
## 5                   0.09576278                3383.793          10492.146
## 6                   0.10161209                3404.712          10243.525
##   L_precuneus_ShapeIndex L_precuneus_Curvedness
## 1              0.2832698             0.10701959
## 2              0.3086211             0.09695860
## 3              0.2862202             0.11096862
## 4              0.2799505             0.09913154
## 5              0.2971880             0.09365830
## 6              0.2842773             0.08811536
##   R_precuneus_AvgMeanCurvature R_precuneus_ComputeArea R_precuneus_Volume
## 1                   0.09441046                3387.310          12464.342
## 2                   0.10789248                3332.431          11293.901
## 3                   0.13150418                2799.881           8080.517
## 4                   0.10829975                3435.362          11166.362
## 5                   0.09613719                3556.810          11808.917
## 6                   0.09127127                4114.963          14350.119
##   R_precuneus_ShapeIndex R_precuneus_Curvedness
## 1              0.2879712             0.09666886
## 2              0.3032337             0.09921845
## 3              0.3310782             0.11408704
## 4              0.3263887             0.09054042
## 5              0.2982102             0.09661751
## 6              0.3037840             0.08448501
##   L_superior_occipital_gyrus_AvgMeanCurvature
## 1                                   0.1195798
## 2                                   0.1205780
## 3                                   0.1129942
## 4                                   0.1046885
## 5                                   0.1191842
## 6                                   0.1181061
##   L_superior_occipital_gyrus_ComputeArea L_superior_occipital_gyrus_Volume
## 1                               2561.545                          7294.012
## 2                               1909.412                          5150.974
## 3                               2008.023                          5697.149
## 4                               2412.866                          7512.356
## 5                               2060.643                          5664.248
## 6                               1854.029                          5149.896
##   L_superior_occipital_gyrus_ShapeIndex
## 1                             0.2949458
## 2                             0.2719930
## 3                             0.2651365
## 4                             0.2711364
## 5                             0.3079957
## 6                             0.2666291
##   L_superior_occipital_gyrus_Curvedness
## 1                             0.1393213
## 2                             0.1500819
## 3                             0.1310171
## 4                             0.1362769
## 5                             0.1426280
## 6                             0.1456626
##   R_superior_occipital_gyrus_AvgMeanCurvature
## 1                                   0.1087897
## 2                                   0.1171069
## 3                                   0.1037152
## 4                                   0.1320050
## 5                                   0.1404328
## 6                                   0.1168706
##   R_superior_occipital_gyrus_ComputeArea R_superior_occipital_gyrus_Volume
## 1                               2564.923                          6882.760
## 2                               2173.619                          6231.256
## 3                               2579.026                          7324.230
## 4                               2079.545                          5355.727
## 5                               1893.186                          4682.705
## 6                               2202.703                          5808.980
##   R_superior_occipital_gyrus_ShapeIndex
## 1                             0.2609457
## 2                             0.2585772
## 3                             0.2641015
## 4                             0.3012312
## 5                             0.2889157
## 6                             0.2803689
##   R_superior_occipital_gyrus_Curvedness
## 1                             0.1488038
## 2                             0.1520477
## 3                             0.1623094
## 4                             0.1615290
## 5                             0.1520513
## 6                             0.1563103
##   L_middle_occipital_gyrus_AvgMeanCurvature
## 1                                0.09196750
## 2                                0.08442675
## 3                                0.09127597
## 4                                0.08336854
## 5                                0.09361627
## 6                                0.09248868
##   L_middle_occipital_gyrus_ComputeArea L_middle_occipital_gyrus_Volume
## 1                             4264.960                        15722.27
## 2                             4503.611                        17128.71
## 3                             3955.185                        14555.55
## 4                             4740.876                        19821.23
## 5                             4229.802                        15466.30
## 6                             4528.289                        16743.73
##   L_middle_occipital_gyrus_ShapeIndex L_middle_occipital_gyrus_Curvedness
## 1                           0.3160000                          0.09652114
## 2                           0.3417904                          0.08082197
## 3                           0.3040396                          0.08682547
## 4                           0.2885401                          0.09235392
## 5                           0.3201293                          0.09023690
## 6                           0.3066691                          0.08634961
##   R_middle_occipital_gyrus_AvgMeanCurvature
## 1                                0.09389006
## 2                                0.09667509
## 3                                0.09152445
## 4                                0.09479980
## 5                                0.09341706
## 6                                0.09855936
##   R_middle_occipital_gyrus_ComputeArea R_middle_occipital_gyrus_Volume
## 1                             4827.668                        17938.67
## 2                             5311.343                        20127.27
## 3                             4945.606                        19244.09
## 4                             4430.510                        16604.35
## 5                             4372.664                        15408.93
## 6                             5884.962                        21090.49
##   R_middle_occipital_gyrus_ShapeIndex R_middle_occipital_gyrus_Curvedness
## 1                           0.3035519                          0.09360675
## 2                           0.3181087                          0.08639906
## 3                           0.3171960                          0.09104467
## 4                           0.3185526                          0.09902467
## 5                           0.2987557                          0.09306130
## 6                           0.3683309                          0.07721975
##   L_inferior_occipital_gyrus_AvgMeanCurvature
## 1                                   0.1157437
## 2                                   0.1102742
## 3                                   0.1137141
## 4                                   0.1133252
## 5                                   0.1071762
## 6                                   0.1132877
##   L_inferior_occipital_gyrus_ComputeArea L_inferior_occipital_gyrus_Volume
## 1                               2518.832                          7449.263
## 2                               2575.385                          7956.538
## 3                               2371.204                          6598.951
## 4                               2990.778                          9397.859
## 5                               2649.330                          8162.506
## 6                               2613.085                          8295.724
##   L_inferior_occipital_gyrus_ShapeIndex
## 1                             0.3156508
## 2                             0.3179899
## 3                             0.3162082
## 4                             0.2986863
## 5                             0.2859327
## 6                             0.3054663
##   L_inferior_occipital_gyrus_Curvedness
## 1                             0.1125443
## 2                             0.1061467
## 3                             0.0936433
## 4                             0.1164720
## 5                             0.1064660
## 6                             0.1089161
##   R_inferior_occipital_gyrus_AvgMeanCurvature
## 1                                  0.09804650
## 2                                  0.08905351
## 3                                  0.09975755
## 4                                  0.10061581
## 5                                  0.09822466
## 6                                  0.11223317
##   R_inferior_occipital_gyrus_ComputeArea R_inferior_occipital_gyrus_Volume
## 1                               2984.339                         10226.646
## 2                               3322.390                         12708.507
## 3                               2778.404                          9224.226
## 4                               2851.548                          9282.553
## 5                               3010.978                         10378.511
## 6                               2944.898                          9461.373
##   R_inferior_occipital_gyrus_ShapeIndex
## 1                             0.3049062
## 2                             0.3491609
## 3                             0.3147194
## 4                             0.3003561
## 5                             0.3038200
## 6                             0.3234459
##   R_inferior_occipital_gyrus_Curvedness L_cuneus_AvgMeanCurvature
## 1                            0.08907501                 0.1156776
## 2                            0.07681380                 0.1215609
## 3                            0.08843280                 0.1153973
## 4                            0.09368360                 0.1151997
## 5                            0.09392322                 0.1259525
## 6                            0.09704642                 0.1202144
##   L_cuneus_ComputeArea L_cuneus_Volume L_cuneus_ShapeIndex
## 1             3138.689        9618.492           0.3003197
## 2             2430.494        6097.885           0.3004880
## 3             2313.170        6014.666           0.2840494
## 4             2319.499        5829.940           0.2748422
## 5             2261.542        5420.857           0.2868048
## 6             2458.758        5870.765           0.2983612
##   L_cuneus_Curvedness R_cuneus_AvgMeanCurvature R_cuneus_ComputeArea
## 1           0.1077938                0.10219094             3519.513
## 2           0.1215284                0.10529532             2722.789
## 3           0.1151975                0.11698650             2621.120
## 4           0.1400617                0.11343918             2494.251
## 5           0.1352942                0.10537895             2782.892
## 6           0.1222192                0.08870164             2762.852
##   R_cuneus_Volume R_cuneus_ShapeIndex R_cuneus_Curvedness
## 1       11940.071           0.3023419           0.1016638
## 2        8342.228           0.2938111           0.1017114
## 3        7704.615           0.2649785           0.1338569
## 4        7534.842           0.2746295           0.1285215
## 5        8066.804           0.2726736           0.1171792
## 6        7842.051           0.2344456           0.1397076
##   L_superior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.08533024
## 2                                 0.08818216
## 3                                 0.09173026
## 4                                 0.07776233
## 5                                 0.08349276
## 6                                 0.08078913
##   L_superior_temporal_gyrus_ComputeArea L_superior_temporal_gyrus_Volume
## 1                              6635.644                         26860.47
## 2                              7677.646                         32329.76
## 3                              6158.281                         23263.73
## 4                              6995.225                         29718.22
## 5                              6772.355                         26337.94
## 6                              7671.939                         32911.09
##   L_superior_temporal_gyrus_ShapeIndex
## 1                            0.3783706
## 2                            0.3832396
## 3                            0.3619839
## 4                            0.3903924
## 5                            0.3598613
## 6                            0.3658588
##   L_superior_temporal_gyrus_Curvedness
## 1                           0.07048535
## 2                           0.06207907
## 3                           0.07330941
## 4                           0.06313585
## 5                           0.06630546
## 6                           0.06012147
##   R_superior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.08869901
## 2                                 0.08121426
## 3                                 0.09115610
## 4                                 0.08373479
## 5                                 0.08799037
## 6                                 0.08795319
##   R_superior_temporal_gyrus_ComputeArea R_superior_temporal_gyrus_Volume
## 1                              5995.017                         24386.22
## 2                              6343.222                         26888.90
## 3                              5446.194                         20156.59
## 4                              6260.992                         25252.26
## 5                              5778.582                         22021.75
## 6                              6905.909                         26694.02
##   R_superior_temporal_gyrus_ShapeIndex
## 1                            0.3649489
## 2                            0.3733774
## 3                            0.3470211
## 4                            0.3920464
## 5                            0.3671237
## 6                            0.3715455
##   R_superior_temporal_gyrus_Curvedness
## 1                           0.06542411
## 2                           0.06523898
## 3                           0.07907334
## 4                           0.05600856
## 5                           0.06634440
## 6                           0.06216614
##   L_middle_temporal_gyrus_AvgMeanCurvature
## 1                               0.13577196
## 2                               0.10573145
## 3                               0.12981117
## 4                               0.09540415
## 5                               0.10457954
## 6                               0.10548477
##   L_middle_temporal_gyrus_ComputeArea L_middle_temporal_gyrus_Volume
## 1                            5233.565                       16947.69
## 2                            5470.255                       17208.84
## 3                            5325.748                       17144.86
## 4                            5574.003                       16750.46
## 5                            5358.926                       15552.00
## 6                            6736.122                       24755.54
##   L_middle_temporal_gyrus_ShapeIndex L_middle_temporal_gyrus_Curvedness
## 1                          0.2918232                         0.13046893
## 2                          0.3291948                         0.08871739
## 3                          0.2944165                         0.09009954
## 4                          0.3190153                         0.08547634
## 5                          0.3192232                         0.08140095
## 6                          0.3021110                         0.08742789
##   R_middle_temporal_gyrus_AvgMeanCurvature
## 1                               0.09881832
## 2                               0.09784834
## 3                               0.09662573
## 4                               0.09304032
## 5                               0.11314295
## 6                               0.09616611
##   R_middle_temporal_gyrus_ComputeArea R_middle_temporal_gyrus_Volume
## 1                            6130.960                       22232.61
## 2                            6960.965                       27476.33
## 3                            5840.725                       20638.79
## 4                            7021.523                       27743.97
## 5                            6097.444                       21165.43
## 6                            7028.058                       25797.53
##   R_middle_temporal_gyrus_ShapeIndex R_middle_temporal_gyrus_Curvedness
## 1                          0.3372119                         0.07372350
## 2                          0.3180938                         0.07262339
## 3                          0.2952768                         0.08719198
## 4                          0.3164606                         0.07635997
## 5                          0.3289957                         0.08069239
## 6                          0.3185178                         0.07104691
##   L_inferior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.08387626
## 2                                 0.08440291
## 3                                 0.15046303
## 4                                 0.08386965
## 5                                 0.08181475
## 6                                 0.08854481
##   L_inferior_temporal_gyrus_ComputeArea L_inferior_temporal_gyrus_Volume
## 1                              5425.194                         21706.26
## 2                              5925.988                         24980.90
## 3                              5455.426                         21813.93
## 4                              6033.020                         25337.60
## 5                              5764.396                         24265.72
## 6                              6161.727                         24965.63
##   L_inferior_temporal_gyrus_ShapeIndex
## 1                            0.3529576
## 2                            0.3863400
## 3                            0.3633563
## 4                            0.3818763
## 5                            0.3801266
## 6                            0.3633352
##   L_inferior_temporal_gyrus_Curvedness
## 1                           0.08126605
## 2                           0.06998834
## 3                           0.08530215
## 4                           0.06878814
## 5                           0.06386685
## 6                           0.07705876
##   R_inferior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.09733136
## 2                                 0.14309865
## 3                                 0.09224883
## 4                                 0.09705139
## 5                                 0.09015700
## 6                                 0.09348744
##   R_inferior_temporal_gyrus_ComputeArea R_inferior_temporal_gyrus_Volume
## 1                              4889.915                         16930.42
## 2                              5113.919                         18076.97
## 3                              4968.181                         18178.27
## 4                              5406.621                         18588.60
## 5                              4977.797                         18143.35
## 6                              6347.293                         23908.35
##   R_inferior_temporal_gyrus_ShapeIndex
## 1                            0.3653207
## 2                            0.3730978
## 3                            0.3642670
## 4                            0.3726786
## 5                            0.3547782
## 6                            0.3643752
##   R_inferior_temporal_gyrus_Curvedness
## 1                           0.07721288
## 2                           0.09922728
## 3                           0.07650701
## 4                           0.07453465
## 5                           0.07617285
## 6                           0.07768165
##   L_parahippocampal_gyrus_AvgMeanCurvature
## 1                                0.1058454
## 2                                0.1077122
## 3                                0.1155507
## 4                                0.1155695
## 5                                0.1051995
## 6                                0.1090259
##   L_parahippocampal_gyrus_ComputeArea L_parahippocampal_gyrus_Volume
## 1                            2575.285                       7266.162
## 2                            2844.754                       7480.951
## 3                            2255.258                       5632.681
## 4                            2282.834                       5927.611
## 5                            2486.467                       6690.719
## 6                            3000.342                       8537.208
##   L_parahippocampal_gyrus_ShapeIndex L_parahippocampal_gyrus_Curvedness
## 1                          0.2775562                          0.1167113
## 2                          0.2607401                          0.1022136
## 3                          0.2680552                          0.1288539
## 4                          0.2918659                          0.1136002
## 5                          0.2689256                          0.1214095
## 6                          0.2985118                          0.1031911
##   R_parahippocampal_gyrus_AvgMeanCurvature
## 1                               0.09920542
## 2                               0.10265286
## 3                               0.10990323
## 4                               0.10331920
## 5                               0.10237843
## 6                               0.10002774
##   R_parahippocampal_gyrus_ComputeArea R_parahippocampal_gyrus_Volume
## 1                            2847.448                       8022.121
## 2                            3198.464                       9512.674
## 3                            2831.426                       7244.603
## 4                            2852.929                       7751.758
## 5                            2909.676                       8168.243
## 6                            4216.187                      12961.197
##   R_parahippocampal_gyrus_ShapeIndex R_parahippocampal_gyrus_Curvedness
## 1                          0.2625498                         0.10588548
## 2                          0.3130394                         0.09406152
## 3                          0.2706445                         0.11459741
## 4                          0.2843905                         0.11661233
## 5                          0.2913733                         0.10670050
## 6                          0.2892527                         0.08910739
##   L_lingual_gyrus_AvgMeanCurvature L_lingual_gyrus_ComputeArea
## 1                       0.09325381                    4064.914
## 2                       0.09506937                    3990.686
## 3                       0.10162731                    3147.679
## 4                       0.08526740                    4111.653
## 5                       0.09714551                    3414.919
## 6                       0.09066825                    3527.309
##   L_lingual_gyrus_Volume L_lingual_gyrus_ShapeIndex
## 1               15295.09                  0.3398995
## 2               15329.18                  0.3268375
## 3               10175.86                  0.3332995
## 4               15891.62                  0.3302158
## 5               11521.30                  0.3171585
## 6               12886.17                  0.3350441
##   L_lingual_gyrus_Curvedness R_lingual_gyrus_AvgMeanCurvature
## 1                 0.07595673                       0.08326412
## 2                 0.08228135                       0.08600172
## 3                 0.08935409                       0.09665706
## 4                 0.07737984                       0.09421878
## 5                 0.08903558                       0.09192208
## 6                 0.08423320                       0.09375447
##   R_lingual_gyrus_ComputeArea R_lingual_gyrus_Volume
## 1                    4296.131               17798.51
## 2                    4208.788               16959.60
## 3                    3310.970               12100.64
## 4                    3764.841               14056.34
## 5                    3714.116               13833.59
## 6                    3956.547               15209.61
##   R_lingual_gyrus_ShapeIndex R_lingual_gyrus_Curvedness
## 1                  0.3224243                 0.07223333
## 2                  0.3203310                 0.07572543
## 3                  0.3205029                 0.08572730
## 4                  0.2945016                 0.09222344
## 5                  0.3098974                 0.09112668
## 6                  0.3258160                 0.08625550
##   L_fusiform_gyrus_AvgMeanCurvature L_fusiform_gyrus_ComputeArea
## 1                        0.10196499                     4239.945
## 2                        0.10385320                     4534.707
## 3                        0.10405280                     4013.385
## 4                        0.11326566                     3902.592
## 5                        0.11218079                     4120.621
## 6                        0.09365524                     4864.410
##   L_fusiform_gyrus_Volume L_fusiform_gyrus_ShapeIndex
## 1                14728.60                   0.3083931
## 2                15830.32                   0.3102792
## 3                12677.99                   0.2857870
## 4                11525.38                   0.2983204
## 5                13775.00                   0.3584661
## 6                17467.13                   0.2929722
##   L_fusiform_gyrus_Curvedness R_fusiform_gyrus_AvgMeanCurvature
## 1                  0.08787598                         0.1003429
## 2                  0.08341972                         0.1063175
## 3                  0.10808808                         0.1267130
## 4                  0.09976534                         0.1076625
## 5                  0.09042557                         0.1018607
## 6                  0.09020279                         0.1199351
##   R_fusiform_gyrus_ComputeArea R_fusiform_gyrus_Volume
## 1                     3934.233                13339.14
## 2                     3945.037                14471.84
## 3                     3551.876                11263.23
## 4                     4260.940                14213.62
## 5                     3919.842                14405.84
## 6                     5169.535                17455.32
##   R_fusiform_gyrus_ShapeIndex R_fusiform_gyrus_Curvedness Sex Weight
## 1                   0.3381375                  0.08972141   2   64.0
## 2                   0.3592094                  0.07762280   1   74.2
## 3                   0.3331986                  0.10994359   2   70.6
## 4                   0.3515383                  0.08235058   2   82.0
## 5                   0.3487578                  0.09018205   1   81.6
## 6                   0.3855645                  0.07418299   2   69.1
##   ResearchGroup VisitID     Age chr12_rs34637584_GT chr12_rs34637584_DP
## 1       Control       1 69.1781                   0                  24
## 2            PD       1 65.1808                   0                  23
## 3            PD       1 67.6247                   0                  24
## 4            PD       1 56.7562                   0                  23
## 5       Control       1 59.4548                   0                  24
## 6            PD       1 57.5781                   0                  20
##   chr12_rs34637584_GQ chr17_rs11868035_GT chr17_rs11868035_DP
## 1                  66                   1                  70
## 2                  69                   1                  53
## 3                  60                   1                  67
## 4                  60                   1                 106
## 5                  60                   1                 120
## 6                  60                   0                  31
##   chr17_rs11868035_GQ chr17_rs11012_GT chr17_rs11012_DP chr17_rs11012_GQ
## 1                  99                1               55               99
## 2                  99                1               60               99
## 3                  99                0               26               66
## 4                  99                1               70               99
## 5                  99                1               67               99
## 6                  70                1               41               99
##   chr17_rs393152_GT chr17_rs393152_DP chr17_rs393152_GQ
## 1                 1                27                99
## 2                 1                15                99
## 3                 0                28                78
## 4                 1                23                77
## 5                 1                30                99
## 6                 1                 9                33
##   chr17_rs12185268_GT chr17_rs12185268_DP chr17_rs12185268_GQ
## 1                   1                  68                  99
## 2                   1                  65                  99
## 3                   0                  27                  66
## 4                   1                  69                  99
## 5                   1                  76                  99
## 6                   1                  47                  99
##   chr17_rs199533_GT chr17_rs199533_DP chr17_rs199533_GQ
## 1                 1                59                99
## 2                 0                20                60
## 3                 0                26                66
## 4                 1                65                99
## 5                 1                55                99
## 6                 1                33                99
##   chr12_rs34637584_AD_1 chr12_rs34637584_AD_2 chr17_rs11868035_AD_1
## 1                    24                     0                    28
## 2                    23                     0                    32
## 3                    24                     0                    32
## 4                    23                     0                    58
## 5                    24                     0                    64
## 6                    20                     0                    31
##   chr17_rs11868035_AD_2 chr17_rs11012_AD_1 chr17_rs11012_AD_2
## 1                    42                 23                 32
## 2                    21                 32                 28
## 3                    35                 26                  0
## 4                    48                 24                 46
## 5                    56                 32                 35
## 6                     0                 19                 22
##   chr17_rs393152_AD_1 chr17_rs393152_AD_2 chr17_rs12185268_AD_1
## 1                  16                  11                    41
## 2                  10                   5                    27
## 3                  28                   0                    27
## 4                   5                  18                    35
## 5                  21                   9                    53
## 6                   2                   7                    29
##   chr17_rs12185268_AD_2 chr17_rs199533_AD_1 chr17_rs199533_AD_2
## 1                    27                  24                  35
## 2                    38                  20                   0
## 3                     0                  26                   0
## 4                    34                  33                  32
## 5                    23                  31                  24
## 6                    18                  17                  16
##   chr12_rs34637584_PL_1 chr12_rs34637584_PL_2 chr12_rs34637584_PL_3
## 1                     0                    66                   681
## 2                     0                    69                   726
## 3                     0                    60                   759
## 4                     0                    60                   857
## 5                     0                    60                   762
## 6                     0                    60                   587
##   chr17_rs11868035_PL_1 chr17_rs11868035_PL_2 chr17_rs11868035_PL_3
## 1                   982                     0                   645
## 2                   498                     0                   848
## 3                   870                     0                   809
## 4                  1028                     0                  1504
## 5                  1219                     0                  1636
## 6                     0                    70                   936
##   chr17_rs11012_PL_1 chr17_rs11012_PL_2 chr17_rs11012_PL_3
## 1                737                  0                549
## 2                679                  0                735
## 3                  0                 66                990
## 4               1125                  0                494
## 5                839                  0                678
## 6                511                  0                485
##   chr17_rs393152_PL_1 chr17_rs393152_PL_2 chr17_rs393152_PL_3
## 1                 249                   0                 372
## 2                 140                   0                 242
## 3                   0                  78                 809
## 4                 437                   0                  77
## 5                 168                   0                 529
## 6                 201                   0                  33
##   chr17_rs12185268_PL_1 chr17_rs12185268_PL_2 chr17_rs12185268_PL_3
## 1                   590                     0                   971
## 2                  1013                     0                   616
## 3                     0                    66                   903
## 4                   809                     0                   837
## 5                   499                     0                  1310
## 6                   380                     0                   672
##   chr17_rs199533_PL_1 chr17_rs199533_PL_2 chr17_rs199533_PL_3
## 1                 939                   0                 545
## 2                   0                  60                 709
## 3                   0                  66                 847
## 4                 810                   0                 925
## 5                 556                   0                 796
## 6                 386                   0                 408
##   UPDRS_Part_I_Summary_Score_Baseline UPDRS_Part_I_Summary_Score_Month_03
## 1                                  NA                                  NA
## 2                                   0                                   0
## 3                                   3                                   2
## 4                                   1                                   1
## 5                                   0                                  NA
## 6                                   1                                   2
##   UPDRS_Part_I_Summary_Score_Month_06 UPDRS_Part_I_Summary_Score_Month_09
## 1                                  NA                                  NA
## 2                                   0                                   1
## 3                                  NA                                   1
## 4                                   0                                   0
## 5                                  NA                                  NA
## 6                                   0                                   1
##   UPDRS_Part_I_Summary_Score_Month_12 UPDRS_Part_I_Summary_Score_Month_18
## 1                                  NA                                  NA
## 2                                   4                                   1
## 3                                   3                                   4
## 4                                   0                                  NA
## 5                                   0                                  NA
## 6                                   2                                  NA
##   UPDRS_Part_I_Summary_Score_Month_24 UPDRS_Part_I_Summary_Score_Month_30
## 1                                  NA                                  NA
## 2                                   0                                   0
## 3                                   8                                   4
## 4                                   0                                   3
## 5                                   1                                  NA
## 6                                  NA                                  NA
##   UPDRS_Part_I_Summary_Score_Month_36 UPDRS_Part_I_Summary_Score_Month_42
## 1                                  NA                                  NA
## 2                                   1                                   1
## 3                                   4                                   6
## 4                                   2                                   0
## 5                                   1                                  NA
## 6                                  NA                                  NA
##   UPDRS_Part_I_Summary_Score_Month_48 UPDRS_Part_I_Summary_Score_Month_54
## 1                                  NA                                  NA
## 2                                   1                                  NA
## 3                                   5                                  NA
## 4                                   0                                  NA
## 5                                   0                                  NA
## 6                                  NA                                  NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline
## 1                                                         NA
## 2                                                          2
## 3                                                         15
## 4                                                          6
## 5                                                          0
## 6                                                          4
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_03
## 1                                                         NA
## 2                                                          2
## 3                                                         10
## 4                                                          5
## 5                                                         NA
## 6                                                         10
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_06
## 1                                                         NA
## 2                                                          3
## 3                                                         NA
## 4                                                          3
## 5                                                         NA
## 6                                                         10
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_09
## 1                                                         NA
## 2                                                          3
## 3                                                         16
## 4                                                          8
## 5                                                         NA
## 6                                                          8
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_12
## 1                                                         NA
## 2                                                          3
## 3                                                         15
## 4                                                          5
## 5                                                          0
## 6                                                         13
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_18
## 1                                                         NA
## 2                                                          4
## 3                                                         16
## 4                                                         NA
## 5                                                         NA
## 6                                                         NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_24
## 1                                                         NA
## 2                                                          2
## 3                                                         14
## 4                                                          7
## 5                                                          0
## 6                                                         NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_30
## 1                                                         NA
## 2                                                          5
## 3                                                         13
## 4                                                          7
## 5                                                         NA
## 6                                                         NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_36
## 1                                                         NA
## 2                                                          6
## 3                                                         16
## 4                                                         10
## 5                                                          0
## 6                                                         NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_42
## 1                                                         NA
## 2                                                         11
## 3                                                         14
## 4                                                         13
## 5                                                         NA
## 6                                                         NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_48
## 1                                                         NA
## 2                                                          5
## 3                                                         18
## 4                                                         10
## 5                                                          0
## 6                                                         NA
##   UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Month_54
## 1                                                         NA
## 2                                                         NA
## 3                                                         NA
## 4                                                         NA
## 5                                                         NA
## 6                                                         NA
##   UPDRS_Part_III_Summary_Score_Baseline
## 1                                    NA
## 2                                    12
## 3                                    17
## 4                                    29
## 5                                     2
## 6                                    22
##   UPDRS_Part_III_Summary_Score_Month_03
## 1                                    NA
## 2                                    18
## 3                                    22
## 4                                    37
## 5                                    NA
## 6                                    30
##   UPDRS_Part_III_Summary_Score_Month_06
## 1                                    NA
## 2                                    23
## 3                                    NA
## 4                                    37
## 5                                    NA
## 6                                    31
##   UPDRS_Part_III_Summary_Score_Month_09
## 1                                    NA
## 2                                    19
## 3                                    20
## 4                                    33
## 5                                    NA
## 6                                    32
##   UPDRS_Part_III_Summary_Score_Month_12
## 1                                    NA
## 2                                    20
## 3                                    27
## 4                                    44
## 5                                     3
## 6                                    33
##   UPDRS_Part_III_Summary_Score_Month_18
## 1                                    NA
## 2                                    29
## 3                                    22
## 4                                    NA
## 5                                    NA
## 6                                    NA
##   UPDRS_Part_III_Summary_Score_Month_24
## 1                                    NA
## 2                                    39
## 3                                    22
## 4                                    43
## 5                                     7
## 6                                    NA
##   UPDRS_Part_III_Summary_Score_Month_30
## 1                                    NA
## 2                                    25
## 3                                    24
## 4                                    37
## 5                                    NA
## 6                                    NA
##   UPDRS_Part_III_Summary_Score_Month_36
## 1                                    NA
## 2                                    34
## 3                                    31
## 4                                    46
## 5                                     6
## 6                                    NA
##   UPDRS_Part_III_Summary_Score_Month_42
## 1                                    NA
## 2                                    42
## 3                                    19
## 4                                    47
## 5                                    NA
## 6                                    NA
##   UPDRS_Part_III_Summary_Score_Month_48
## 1                                    NA
## 2                                    39
## 3                                    29
## 4                                    59
## 5                                     1
## 6                                    NA
##   UPDRS_Part_III_Summary_Score_Month_54
## 1                                    NA
## 2                                    NA
## 3                                    NA
## 4                                    NA
## 5                                    NA
## 6                                    NA
##   UPDRS_Part_IV_Summary_Score_Baseline
## 1                                   NA
## 2                                   NA
## 3                                   NA
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_03
## 1                                   NA
## 2                                   NA
## 3                                   NA
## 4                                   NA
## 5                                   NA
## 6                                    0
##   UPDRS_Part_IV_Summary_Score_Month_06
## 1                                   NA
## 2                                   NA
## 3                                   NA
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_09
## 1                                   NA
## 2                                   NA
## 3                                   NA
## 4                                   NA
## 5                                   NA
## 6                                    0
##   UPDRS_Part_IV_Summary_Score_Month_12
## 1                                   NA
## 2                                   NA
## 3                                    0
## 4                                   NA
## 5                                   NA
## 6                                    0
##   UPDRS_Part_IV_Summary_Score_Month_18
## 1                                   NA
## 2                                   NA
## 3                                    0
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_24
## 1                                   NA
## 2                                   NA
## 3                                    0
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_30
## 1                                   NA
## 2                                   NA
## 3                                    1
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_36
## 1                                   NA
## 2                                   NA
## 3                                    4
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_42
## 1                                   NA
## 2                                    0
## 3                                    4
## 4                                    0
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_48
## 1                                   NA
## 2                                    0
## 3                                    3
## 4                                    0
## 5                                   NA
## 6                                   NA
##   UPDRS_Part_IV_Summary_Score_Month_54
## 1                                   NA
## 2                                   NA
## 3                                   NA
## 4                                   NA
## 5                                   NA
## 6                                   NA
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Baseline
## 1                                                                     NA
## 2                                                                      6
## 3                                                                     14
## 4                                                                      8
## 5                                                                      6
## 6                                                                      0
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_06
## 1                                                                     NA
## 2                                                                      7
## 3                                                                     NA
## 4                                                                      8
## 5                                                                     NA
## 6                                                                      0
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_09
## 1                                                                     NA
## 2                                                                     NA
## 3                                                                     NA
## 4                                                                     NA
## 5                                                                     NA
## 6                                                                     NA
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_12
## 1                                                                     NA
## 2                                                                      3
## 3                                                                     14
## 4                                                                      6
## 5                                                                      6
## 6                                                                      6
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_18
## 1                                                                     NA
## 2                                                                     NA
## 3                                                                     NA
## 4                                                                     NA
## 5                                                                     NA
## 6                                                                     NA
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_24
## 1                                                                     NA
## 2                                                                      7
## 3                                                                     11
## 4                                                                      7
## 5                                                                     10
## 6                                                                     NA
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_36
## 1                                                                     NA
## 2                                                                      5
## 3                                                                     14
## 4                                                                      7
## 5                                                                     11
## 6                                                                     NA
##   X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Month_48
## 1                                                                     NA
## 2                                                                      6
## 3                                                                     17
## 4                                                                      6
## 5                                                                     10
## 6                                                                     NA
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline
## 1                                                                                 NA
## 2                                                                                  6
## 3                                                                                  6
## 4                                                                                  4
## 5                                                                                  5
## 6                                                                                  5
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_06
## 1                                                                                 NA
## 2                                                                                  4
## 3                                                                                 NA
## 4                                                                                  4
## 5                                                                                 NA
## 6                                                                                  5
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_09
## 1                                                                                 NA
## 2                                                                                 NA
## 3                                                                                 NA
## 4                                                                                 NA
## 5                                                                                 NA
## 6                                                                                 NA
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_12
## 1                                                                                 NA
## 2                                                                                  5
## 3                                                                                  6
## 4                                                                                  4
## 5                                                                                  4
## 6                                                                                  5
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_18
## 1                                                                                 NA
## 2                                                                                 NA
## 3                                                                                 NA
## 4                                                                                 NA
## 5                                                                                 NA
## 6                                                                                 NA
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_24
## 1                                                                                 NA
## 2                                                                                  5
## 3                                                                                  9
## 4                                                                                  4
## 5                                                                                  6
## 6                                                                                 NA
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_36
## 1                                                                                 NA
## 2                                                                                  7
## 3                                                                                  6
## 4                                                                                  4
## 5                                                                                  5
## 6                                                                                 NA
##   X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Month_48
## 1                                                                                 NA
## 2                                                                                  6
## 3                                                                                  4
## 4                                                                                  5
## 5                                                                                  4
## 6                                                                                 NA
##                   COGSTATE COGDECLN FNCDTCOG    COGDXCL EDUCYRS
## 1 Normal Cognition (PD-NC)       No       No  50% - 89%      18
## 2 Normal Cognition (PD-NC)       No       No 90% - 100%      16
## 3 Normal Cognition (PD-NC)      Yes       No  50% - 89%      16
## 4 Normal Cognition (PD-NC)       No       No  50% - 89%      16
## 5 Normal Cognition (PD-NC)      Yes       No  50% - 89%      16
## 6                     <NA>     <NA>     <NA>       <NA>      14
##   RECRUITMENT_CAT              APPRDX
## 1              HC     Healthy Control
## 2              PD Parkinson's disease
## 3              PD Parkinson's disease
## 4              PD Parkinson's disease
## 5              HC     Healthy Control
## 6              PD Parkinson's disease
#longitudinal analysis
ppmi_longit<-read.csv("ppmi_top_wide_UPDRS.csv",header=TRUE)
clinical<-read.csv("ppmi_clinical.csv",header=TRUE)
merged_dataset<-merge(ppmi_longit,clinical,by="FID_IID",all.x=TRUE)
ppmi_long<-merged_dataset[,c(1:342,351:354,364,365,347)]
head(ppmi_long)
##   FID_IID X.1.x X.x L_insular_cortex_AvgMeanCurvature
## 1    3001     1   2                          0.110445
## 2    3001  4852   2                          0.110445
## 3    3001  2206   2                          0.110445
## 4    3001  2647   2                          0.110445
## 5    3001  3970   2                          0.110445
## 6    3001  1765   2                          0.110445
##   L_insular_cortex_ComputeArea L_insular_cortex_Volume
## 1                     2917.938                8754.107
## 2                     2917.938                8754.107
## 3                     2917.938                8754.107
## 4                     2917.938                8754.107
## 5                     2917.938                8754.107
## 6                     2917.938                8754.107
##   L_insular_cortex_ShapeIndex L_insular_cortex_Curvedness
## 1                   0.3207401                   0.1033839
## 2                   0.3207401                   0.1033839
## 3                   0.3207401                   0.1033839
## 4                   0.3207401                   0.1033839
## 5                   0.3207401                   0.1033839
## 6                   0.3207401                   0.1033839
##   R_insular_cortex_AvgMeanCurvature R_insular_cortex_ComputeArea
## 1                         0.1160668                     2342.961
## 2                         0.1160668                     2342.961
## 3                         0.1160668                     2342.961
## 4                         0.1160668                     2342.961
## 5                         0.1160668                     2342.961
## 6                         0.1160668                     2342.961
##   R_insular_cortex_Volume R_insular_cortex_ShapeIndex
## 1                5732.367                    0.314957
## 2                5732.367                    0.314957
## 3                5732.367                    0.314957
## 4                5732.367                    0.314957
## 5                5732.367                    0.314957
## 6                5732.367                    0.314957
##   R_insular_cortex_Curvedness L_cingulate_gyrus_AvgMeanCurvature
## 1                   0.1215921                          0.1246343
## 2                   0.1215921                          0.1246343
## 3                   0.1215921                          0.1246343
## 4                   0.1215921                          0.1246343
## 5                   0.1215921                          0.1246343
## 6                   0.1215921                          0.1246343
##   L_cingulate_gyrus_ComputeArea L_cingulate_gyrus_Volume
## 1                       4381.93                 11205.13
## 2                       4381.93                 11205.13
## 3                       4381.93                 11205.13
## 4                       4381.93                 11205.13
## 5                       4381.93                 11205.13
## 6                       4381.93                 11205.13
##   L_cingulate_gyrus_ShapeIndex L_cingulate_gyrus_Curvedness
## 1                    0.4349292                   0.06714417
## 2                    0.4349292                   0.06714417
## 3                    0.4349292                   0.06714417
## 4                    0.4349292                   0.06714417
## 5                    0.4349292                   0.06714417
## 6                    0.4349292                   0.06714417
##   R_cingulate_gyrus_AvgMeanCurvature R_cingulate_gyrus_ComputeArea
## 1                          0.1249111                      4610.447
## 2                          0.1249111                      4610.447
## 3                          0.1249111                      4610.447
## 4                          0.1249111                      4610.447
## 5                          0.1249111                      4610.447
## 6                          0.1249111                      4610.447
##   R_cingulate_gyrus_Volume R_cingulate_gyrus_ShapeIndex
## 1                 12246.55                    0.4350192
## 2                 12246.55                    0.4350192
## 3                 12246.55                    0.4350192
## 4                 12246.55                    0.4350192
## 5                 12246.55                    0.4350192
## 6                 12246.55                    0.4350192
##   R_cingulate_gyrus_Curvedness L_caudate_AvgMeanCurvature
## 1                   0.07081687                  0.2392929
## 2                   0.07081687                  0.2392929
## 3                   0.07081687                  0.2392929
## 4                   0.07081687                  0.2392929
## 5                   0.07081687                  0.2392929
## 6                   0.07081687                  0.2392929
##   L_caudate_ComputeArea L_caudate_Volume L_caudate_ShapeIndex
## 1              621.5344         821.8991            0.2473931
## 2              621.5344         821.8991            0.2473931
## 3              621.5344         821.8991            0.2473931
## 4              621.5344         821.8991            0.2473931
## 5              621.5344         821.8991            0.2473931
## 6              621.5344         821.8991            0.2473931
##   L_caudate_Curvedness R_caudate_AvgMeanCurvature R_caudate_ComputeArea
## 1             0.342922                  0.1558452              1302.146
## 2             0.342922                  0.1558452              1302.146
## 3             0.342922                  0.1558452              1302.146
## 4             0.342922                  0.1558452              1302.146
## 5             0.342922                  0.1558452              1302.146
## 6             0.342922                  0.1558452              1302.146
##   R_caudate_Volume R_caudate_ShapeIndex R_caudate_Curvedness
## 1         2526.248            0.2892424            0.1496714
## 2         2526.248            0.2892424            0.1496714
## 3         2526.248            0.2892424            0.1496714
## 4         2526.248            0.2892424            0.1496714
## 5         2526.248            0.2892424            0.1496714
## 6         2526.248            0.2892424            0.1496714
##   L_putamen_AvgMeanCurvature L_putamen_ComputeArea L_putamen_Volume
## 1                  0.2022735              1029.175         1543.017
## 2                  0.2022735              1029.175         1543.017
## 3                  0.2022735              1029.175         1543.017
## 4                  0.2022735              1029.175         1543.017
## 5                  0.2022735              1029.175         1543.017
## 6                  0.2022735              1029.175         1543.017
##   L_putamen_ShapeIndex L_putamen_Curvedness R_putamen_AvgMeanCurvature
## 1            0.2853486            0.2320214                  0.1111208
## 2            0.2853486            0.2320214                  0.1111208
## 3            0.2853486            0.2320214                  0.1111208
## 4            0.2853486            0.2320214                  0.1111208
## 5            0.2853486            0.2320214                  0.1111208
## 6            0.2853486            0.2320214                  0.1111208
##   R_putamen_ComputeArea R_putamen_Volume R_putamen_ShapeIndex
## 1              1680.197         3792.201            0.2670927
## 2              1680.197         3792.201            0.2670927
## 3              1680.197         3792.201            0.2670927
## 4              1680.197         3792.201            0.2670927
## 5              1680.197         3792.201            0.2670927
## 6              1680.197         3792.201            0.2670927
##   R_putamen_Curvedness L_hippocampus_AvgMeanCurvature
## 1            0.1332011                      0.1226265
## 2            0.1332011                      0.1226265
## 3            0.1332011                      0.1226265
## 4            0.1332011                      0.1226265
## 5            0.1332011                      0.1226265
## 6            0.1332011                      0.1226265
##   L_hippocampus_ComputeArea L_hippocampus_Volume L_hippocampus_ShapeIndex
## 1                  1769.672             4737.038                0.3201427
## 2                  1769.672             4737.038                0.3201427
## 3                  1769.672             4737.038                0.3201427
## 4                  1769.672             4737.038                0.3201427
## 5                  1769.672             4737.038                0.3201427
## 6                  1769.672             4737.038                0.3201427
##   L_hippocampus_Curvedness R_hippocampus_AvgMeanCurvature
## 1                0.1179703                      0.1312485
## 2                0.1179703                      0.1312485
## 3                0.1179703                      0.1312485
## 4                0.1179703                      0.1312485
## 5                0.1179703                      0.1312485
## 6                0.1179703                      0.1312485
##   R_hippocampus_ComputeArea R_hippocampus_Volume R_hippocampus_ShapeIndex
## 1                  1578.946             3817.621                0.2894075
## 2                  1578.946             3817.621                0.2894075
## 3                  1578.946             3817.621                0.2894075
## 4                  1578.946             3817.621                0.2894075
## 5                  1578.946             3817.621                0.2894075
## 6                  1578.946             3817.621                0.2894075
##   R_hippocampus_Curvedness cerebellum_AvgMeanCurvature
## 1                0.1482493                 -0.01081359
## 2                0.1482493                 -0.01081359
## 3                0.1482493                 -0.01081359
## 4                0.1482493                 -0.01081359
## 5                0.1482493                 -0.01081359
## 6                0.1482493                 -0.01081359
##   cerebellum_ComputeArea cerebellum_Volume cerebellum_ShapeIndex
## 1               20909.58          185742.6             0.2932517
## 2               20909.58          185742.6             0.2932517
## 3               20909.58          185742.6             0.2932517
## 4               20909.58          185742.6             0.2932517
## 5               20909.58          185742.6             0.2932517
## 6               20909.58          185742.6             0.2932517
##   cerebellum_Curvedness brainstem_AvgMeanCurvature brainstem_ComputeArea
## 1             0.1674615                 0.06346277              7741.742
## 2             0.1674615                 0.06346277              7741.742
## 3             0.1674615                 0.06346277              7741.742
## 4             0.1674615                 0.06346277              7741.742
## 5             0.1674615                 0.06346277              7741.742
## 6             0.1674615                 0.06346277              7741.742
##   brainstem_Volume brainstem_ShapeIndex brainstem_Curvedness
## 1         45610.19            0.3192699           0.07574226
## 2         45610.19            0.3192699           0.07574226
## 3         45610.19            0.3192699           0.07574226
## 4         45610.19            0.3192699           0.07574226
## 5         45610.19            0.3192699           0.07574226
## 6         45610.19            0.3192699           0.07574226
##   L_superior_frontal_gyrus_AvgMeanCurvature
## 1                                0.07951369
## 2                                0.07951369
## 3                                0.07951369
## 4                                0.07951369
## 5                                0.07951369
## 6                                0.07951369
##   L_superior_frontal_gyrus_ComputeArea L_superior_frontal_gyrus_Volume
## 1                              11363.7                        53308.55
## 2                              11363.7                        53308.55
## 3                              11363.7                        53308.55
## 4                              11363.7                        53308.55
## 5                              11363.7                        53308.55
## 6                              11363.7                        53308.55
##   L_superior_frontal_gyrus_ShapeIndex L_superior_frontal_gyrus_Curvedness
## 1                           0.3744766                          0.05133303
## 2                           0.3744766                          0.05133303
## 3                           0.3744766                          0.05133303
## 4                           0.3744766                          0.05133303
## 5                           0.3744766                          0.05133303
## 6                           0.3744766                          0.05133303
##   R_superior_frontal_gyrus_AvgMeanCurvature
## 1                                0.08691916
## 2                                0.08691916
## 3                                0.08691916
## 4                                0.08691916
## 5                                0.08691916
## 6                                0.08691916
##   R_superior_frontal_gyrus_ComputeArea R_superior_frontal_gyrus_Volume
## 1                             11134.17                        52396.24
## 2                             11134.17                        52396.24
## 3                             11134.17                        52396.24
## 4                             11134.17                        52396.24
## 5                             11134.17                        52396.24
## 6                             11134.17                        52396.24
##   R_superior_frontal_gyrus_ShapeIndex R_superior_frontal_gyrus_Curvedness
## 1                           0.4484875                          0.04586595
## 2                           0.4484875                          0.04586595
## 3                           0.4484875                          0.04586595
## 4                           0.4484875                          0.04586595
## 5                           0.4484875                          0.04586595
## 6                           0.4484875                          0.04586595
##   L_middle_frontal_gyrus_AvgMeanCurvature
## 1                               0.1195262
## 2                               0.1195262
## 3                               0.1195262
## 4                               0.1195262
## 5                               0.1195262
## 6                               0.1195262
##   L_middle_frontal_gyrus_ComputeArea L_middle_frontal_gyrus_Volume
## 1                           9988.897                      52452.81
## 2                           9988.897                      52452.81
## 3                           9988.897                      52452.81
## 4                           9988.897                      52452.81
## 5                           9988.897                      52452.81
## 6                           9988.897                      52452.81
##   L_middle_frontal_gyrus_ShapeIndex L_middle_frontal_gyrus_Curvedness
## 1                         0.3481521                        0.06595413
## 2                         0.3481521                        0.06595413
## 3                         0.3481521                        0.06595413
## 4                         0.3481521                        0.06595413
## 5                         0.3481521                        0.06595413
## 6                         0.3481521                        0.06595413
##   R_middle_frontal_gyrus_AvgMeanCurvature
## 1                              0.07785072
## 2                              0.07785072
## 3                              0.07785072
## 4                              0.07785072
## 5                              0.07785072
## 6                              0.07785072
##   R_middle_frontal_gyrus_ComputeArea R_middle_frontal_gyrus_Volume
## 1                           9660.306                      54012.12
## 2                           9660.306                      54012.12
## 3                           9660.306                      54012.12
## 4                           9660.306                      54012.12
## 5                           9660.306                      54012.12
## 6                           9660.306                      54012.12
##   R_middle_frontal_gyrus_ShapeIndex R_middle_frontal_gyrus_Curvedness
## 1                         0.3178475                        0.05932451
## 2                         0.3178475                        0.05932451
## 3                         0.3178475                        0.05932451
## 4                         0.3178475                        0.05932451
## 5                         0.3178475                        0.05932451
## 6                         0.3178475                        0.05932451
##   L_inferior_frontal_gyrus_AvgMeanCurvature
## 1                                0.08264828
## 2                                0.08264828
## 3                                0.08264828
## 4                                0.08264828
## 5                                0.08264828
## 6                                0.08264828
##   L_inferior_frontal_gyrus_ComputeArea L_inferior_frontal_gyrus_Volume
## 1                             5091.727                        25113.25
## 2                             5091.727                        25113.25
## 3                             5091.727                        25113.25
## 4                             5091.727                        25113.25
## 5                             5091.727                        25113.25
## 6                             5091.727                        25113.25
##   L_inferior_frontal_gyrus_ShapeIndex L_inferior_frontal_gyrus_Curvedness
## 1                           0.3067739                          0.09213249
## 2                           0.3067739                          0.09213249
## 3                           0.3067739                          0.09213249
## 4                           0.3067739                          0.09213249
## 5                           0.3067739                          0.09213249
## 6                           0.3067739                          0.09213249
##   R_inferior_frontal_gyrus_AvgMeanCurvature
## 1                                0.07610716
## 2                                0.07610716
## 3                                0.07610716
## 4                                0.07610716
## 5                                0.07610716
## 6                                0.07610716
##   R_inferior_frontal_gyrus_ComputeArea R_inferior_frontal_gyrus_Volume
## 1                             5612.835                        28546.87
## 2                             5612.835                        28546.87
## 3                             5612.835                        28546.87
## 4                             5612.835                        28546.87
## 5                             5612.835                        28546.87
## 6                             5612.835                        28546.87
##   R_inferior_frontal_gyrus_ShapeIndex R_inferior_frontal_gyrus_Curvedness
## 1                           0.3206594                          0.06914873
## 2                           0.3206594                          0.06914873
## 3                           0.3206594                          0.06914873
## 4                           0.3206594                          0.06914873
## 5                           0.3206594                          0.06914873
## 6                           0.3206594                          0.06914873
##   L_precentral_gyrus_AvgMeanCurvature L_precentral_gyrus_ComputeArea
## 1                          0.09409574                       6634.533
## 2                          0.09409574                       6634.533
## 3                          0.09409574                       6634.533
## 4                          0.09409574                       6634.533
## 5                          0.09409574                       6634.533
## 6                          0.09409574                       6634.533
##   L_precentral_gyrus_Volume L_precentral_gyrus_ShapeIndex
## 1                   25205.3                      0.351831
## 2                   25205.3                      0.351831
## 3                   25205.3                      0.351831
## 4                   25205.3                      0.351831
## 5                   25205.3                      0.351831
## 6                   25205.3                      0.351831
##   L_precentral_gyrus_Curvedness R_precentral_gyrus_AvgMeanCurvature
## 1                    0.09609143                          0.08857492
## 2                    0.09609143                          0.08857492
## 3                    0.09609143                          0.08857492
## 4                    0.09609143                          0.08857492
## 5                    0.09609143                          0.08857492
## 6                    0.09609143                          0.08857492
##   R_precentral_gyrus_ComputeArea R_precentral_gyrus_Volume
## 1                       6057.209                  23691.55
## 2                       6057.209                  23691.55
## 3                       6057.209                  23691.55
## 4                       6057.209                  23691.55
## 5                       6057.209                  23691.55
## 6                       6057.209                  23691.55
##   R_precentral_gyrus_ShapeIndex R_precentral_gyrus_Curvedness
## 1                     0.3654834                    0.07582953
## 2                     0.3654834                    0.07582953
## 3                     0.3654834                    0.07582953
## 4                     0.3654834                    0.07582953
## 5                     0.3654834                    0.07582953
## 6                     0.3654834                    0.07582953
##   L_middle_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                    0.09504461
## 2                                    0.09504461
## 3                                    0.09504461
## 4                                    0.09504461
## 5                                    0.09504461
## 6                                    0.09504461
##   L_middle_orbitofrontal_gyrus_ComputeArea
## 1                                 3190.647
## 2                                 3190.647
## 3                                 3190.647
## 4                                 3190.647
## 5                                 3190.647
## 6                                 3190.647
##   L_middle_orbitofrontal_gyrus_Volume
## 1                            10459.92
## 2                            10459.92
## 3                            10459.92
## 4                            10459.92
## 5                            10459.92
## 6                            10459.92
##   L_middle_orbitofrontal_gyrus_ShapeIndex
## 1                               0.2909523
## 2                               0.2909523
## 3                               0.2909523
## 4                               0.2909523
## 5                               0.2909523
## 6                               0.2909523
##   L_middle_orbitofrontal_gyrus_Curvedness
## 1                              0.08821871
## 2                              0.08821871
## 3                              0.08821871
## 4                              0.08821871
## 5                              0.08821871
## 6                              0.08821871
##   R_middle_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                     0.1093085
## 2                                     0.1093085
## 3                                     0.1093085
## 4                                     0.1093085
## 5                                     0.1093085
## 6                                     0.1093085
##   R_middle_orbitofrontal_gyrus_ComputeArea
## 1                                 3108.103
## 2                                 3108.103
## 3                                 3108.103
## 4                                 3108.103
## 5                                 3108.103
## 6                                 3108.103
##   R_middle_orbitofrontal_gyrus_Volume
## 1                             9611.13
## 2                             9611.13
## 3                             9611.13
## 4                             9611.13
## 5                             9611.13
## 6                             9611.13
##   R_middle_orbitofrontal_gyrus_ShapeIndex
## 1                                0.306004
## 2                                0.306004
## 3                                0.306004
## 4                                0.306004
## 5                                0.306004
## 6                                0.306004
##   R_middle_orbitofrontal_gyrus_Curvedness
## 1                              0.09612964
## 2                              0.09612964
## 3                              0.09612964
## 4                              0.09612964
## 5                              0.09612964
## 6                              0.09612964
##   L_lateral_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                      0.1274801
## 2                                      0.1274801
## 3                                      0.1274801
## 4                                      0.1274801
## 5                                      0.1274801
## 6                                      0.1274801
##   L_lateral_orbitofrontal_gyrus_ComputeArea
## 1                                  1940.454
## 2                                  1940.454
## 3                                  1940.454
## 4                                  1940.454
## 5                                  1940.454
## 6                                  1940.454
##   L_lateral_orbitofrontal_gyrus_Volume
## 1                             4320.333
## 2                             4320.333
## 3                             4320.333
## 4                             4320.333
## 5                             4320.333
## 6                             4320.333
##   L_lateral_orbitofrontal_gyrus_ShapeIndex
## 1                                0.2895921
## 2                                0.2895921
## 3                                0.2895921
## 4                                0.2895921
## 5                                0.2895921
## 6                                0.2895921
##   L_lateral_orbitofrontal_gyrus_Curvedness
## 1                                0.1775847
## 2                                0.1775847
## 3                                0.1775847
## 4                                0.1775847
## 5                                0.1775847
## 6                                0.1775847
##   R_lateral_orbitofrontal_gyrus_AvgMeanCurvature
## 1                                      0.1397253
## 2                                      0.1397253
## 3                                      0.1397253
## 4                                      0.1397253
## 5                                      0.1397253
## 6                                      0.1397253
##   R_lateral_orbitofrontal_gyrus_ComputeArea
## 1                                  1953.675
## 2                                  1953.675
## 3                                  1953.675
## 4                                  1953.675
## 5                                  1953.675
## 6                                  1953.675
##   R_lateral_orbitofrontal_gyrus_Volume
## 1                             4093.492
## 2                             4093.492
## 3                             4093.492
## 4                             4093.492
## 5                             4093.492
## 6                             4093.492
##   R_lateral_orbitofrontal_gyrus_ShapeIndex
## 1                                0.2971379
## 2                                0.2971379
## 3                                0.2971379
## 4                                0.2971379
## 5                                0.2971379
## 6                                0.2971379
##   R_lateral_orbitofrontal_gyrus_Curvedness L_gyrus_rectus_AvgMeanCurvature
## 1                                0.1634671                       0.2078852
## 2                                0.1634671                       0.2078852
## 3                                0.1634671                       0.2078852
## 4                                0.1634671                       0.2078852
## 5                                0.1634671                       0.2078852
## 6                                0.1634671                       0.2078852
##   L_gyrus_rectus_ComputeArea L_gyrus_rectus_Volume
## 1                   1143.078              1785.822
## 2                   1143.078              1785.822
## 3                   1143.078              1785.822
## 4                   1143.078              1785.822
## 5                   1143.078              1785.822
## 6                   1143.078              1785.822
##   L_gyrus_rectus_ShapeIndex L_gyrus_rectus_Curvedness
## 1                 0.2893511                 0.2222131
## 2                 0.2893511                 0.2222131
## 3                 0.2893511                 0.2222131
## 4                 0.2893511                 0.2222131
## 5                 0.2893511                 0.2222131
## 6                 0.2893511                 0.2222131
##   R_gyrus_rectus_AvgMeanCurvature R_gyrus_rectus_ComputeArea
## 1                       0.1519435                   1408.899
## 2                       0.1519435                   1408.899
## 3                       0.1519435                   1408.899
## 4                       0.1519435                   1408.899
## 5                       0.1519435                   1408.899
## 6                       0.1519435                   1408.899
##   R_gyrus_rectus_Volume R_gyrus_rectus_ShapeIndex
## 1              2763.942                  0.261203
## 2              2763.942                  0.261203
## 3              2763.942                  0.261203
## 4              2763.942                  0.261203
## 5              2763.942                  0.261203
## 6              2763.942                  0.261203
##   R_gyrus_rectus_Curvedness L_postcentral_gyrus_AvgMeanCurvature
## 1                 0.1959469                           0.09087086
## 2                 0.1959469                           0.09087086
## 3                 0.1959469                           0.09087086
## 4                 0.1959469                           0.09087086
## 5                 0.1959469                           0.09087086
## 6                 0.1959469                           0.09087086
##   L_postcentral_gyrus_ComputeArea L_postcentral_gyrus_Volume
## 1                        5952.575                   22426.55
## 2                        5952.575                   22426.55
## 3                        5952.575                   22426.55
## 4                        5952.575                   22426.55
## 5                        5952.575                   22426.55
## 6                        5952.575                   22426.55
##   L_postcentral_gyrus_ShapeIndex L_postcentral_gyrus_Curvedness
## 1                      0.3305127                     0.08240747
## 2                      0.3305127                     0.08240747
## 3                      0.3305127                     0.08240747
## 4                      0.3305127                     0.08240747
## 5                      0.3305127                     0.08240747
## 6                      0.3305127                     0.08240747
##   R_postcentral_gyrus_AvgMeanCurvature R_postcentral_gyrus_ComputeArea
## 1                           0.07717761                        6274.401
## 2                           0.07717761                        6274.401
## 3                           0.07717761                        6274.401
## 4                           0.07717761                        6274.401
## 5                           0.07717761                        6274.401
## 6                           0.07717761                        6274.401
##   R_postcentral_gyrus_Volume R_postcentral_gyrus_ShapeIndex
## 1                    26116.1                      0.3320086
## 2                    26116.1                      0.3320086
## 3                    26116.1                      0.3320086
## 4                    26116.1                      0.3320086
## 5                    26116.1                      0.3320086
## 6                    26116.1                      0.3320086
##   R_postcentral_gyrus_Curvedness
## 1                     0.08080232
## 2                     0.08080232
## 3                     0.08080232
## 4                     0.08080232
## 5                     0.08080232
## 6                     0.08080232
##   L_superior_parietal_gyrus_AvgMeanCurvature
## 1                                   0.156426
## 2                                   0.156426
## 3                                   0.156426
## 4                                   0.156426
## 5                                   0.156426
## 6                                   0.156426
##   L_superior_parietal_gyrus_ComputeArea L_superior_parietal_gyrus_Volume
## 1                              5228.112                         22835.86
## 2                              5228.112                         22835.86
## 3                              5228.112                         22835.86
## 4                              5228.112                         22835.86
## 5                              5228.112                         22835.86
## 6                              5228.112                         22835.86
##   L_superior_parietal_gyrus_ShapeIndex
## 1                            0.3180919
## 2                            0.3180919
## 3                            0.3180919
## 4                            0.3180919
## 5                            0.3180919
## 6                            0.3180919
##   L_superior_parietal_gyrus_Curvedness
## 1                           0.08668642
## 2                           0.08668642
## 3                           0.08668642
## 4                           0.08668642
## 5                           0.08668642
## 6                           0.08668642
##   R_superior_parietal_gyrus_AvgMeanCurvature
## 1                                  0.0780768
## 2                                  0.0780768
## 3                                  0.0780768
## 4                                  0.0780768
## 5                                  0.0780768
## 6                                  0.0780768
##   R_superior_parietal_gyrus_ComputeArea R_superior_parietal_gyrus_Volume
## 1                              5121.035                         25387.02
## 2                              5121.035                         25387.02
## 3                              5121.035                         25387.02
## 4                              5121.035                         25387.02
## 5                              5121.035                         25387.02
## 6                              5121.035                         25387.02
##   R_superior_parietal_gyrus_ShapeIndex
## 1                            0.2799022
## 2                            0.2799022
## 3                            0.2799022
## 4                            0.2799022
## 5                            0.2799022
## 6                            0.2799022
##   R_superior_parietal_gyrus_Curvedness
## 1                           0.08711799
## 2                           0.08711799
## 3                           0.08711799
## 4                           0.08711799
## 5                           0.08711799
## 6                           0.08711799
##   L_supramarginal_gyrus_AvgMeanCurvature L_supramarginal_gyrus_ComputeArea
## 1                             0.08960319                           3766.59
## 2                             0.08960319                           3766.59
## 3                             0.08960319                           3766.59
## 4                             0.08960319                           3766.59
## 5                             0.08960319                           3766.59
## 6                             0.08960319                           3766.59
##   L_supramarginal_gyrus_Volume L_supramarginal_gyrus_ShapeIndex
## 1                     14904.22                        0.3068543
## 2                     14904.22                        0.3068543
## 3                     14904.22                        0.3068543
## 4                     14904.22                        0.3068543
## 5                     14904.22                        0.3068543
## 6                     14904.22                        0.3068543
##   L_supramarginal_gyrus_Curvedness R_supramarginal_gyrus_AvgMeanCurvature
## 1                       0.09030263                             0.09359056
## 2                       0.09030263                             0.09359056
## 3                       0.09030263                             0.09359056
## 4                       0.09030263                             0.09359056
## 5                       0.09030263                             0.09359056
## 6                       0.09030263                             0.09359056
##   R_supramarginal_gyrus_ComputeArea R_supramarginal_gyrus_Volume
## 1                          2943.982                     11236.22
## 2                          2943.982                     11236.22
## 3                          2943.982                     11236.22
## 4                          2943.982                     11236.22
## 5                          2943.982                     11236.22
## 6                          2943.982                     11236.22
##   R_supramarginal_gyrus_ShapeIndex R_supramarginal_gyrus_Curvedness
## 1                        0.3043556                         0.113241
## 2                        0.3043556                         0.113241
## 3                        0.3043556                         0.113241
## 4                        0.3043556                         0.113241
## 5                        0.3043556                         0.113241
## 6                        0.3043556                         0.113241
##   L_angular_gyrus_AvgMeanCurvature L_angular_gyrus_ComputeArea
## 1                       0.08332833                    4499.945
## 2                       0.08332833                    4499.945
## 3                       0.08332833                    4499.945
## 4                       0.08332833                    4499.945
## 5                       0.08332833                    4499.945
## 6                       0.08332833                    4499.945
##   L_angular_gyrus_Volume L_angular_gyrus_ShapeIndex
## 1               18707.85                  0.3069968
## 2               18707.85                  0.3069968
## 3               18707.85                  0.3069968
## 4               18707.85                  0.3069968
## 5               18707.85                  0.3069968
## 6               18707.85                  0.3069968
##   L_angular_gyrus_Curvedness R_angular_gyrus_AvgMeanCurvature
## 1                 0.08690669                        0.1024264
## 2                 0.08690669                        0.1024264
## 3                 0.08690669                        0.1024264
## 4                 0.08690669                        0.1024264
## 5                 0.08690669                        0.1024264
## 6                 0.08690669                        0.1024264
##   R_angular_gyrus_ComputeArea R_angular_gyrus_Volume
## 1                    3666.847               13003.38
## 2                    3666.847               13003.38
## 3                    3666.847               13003.38
## 4                    3666.847               13003.38
## 5                    3666.847               13003.38
## 6                    3666.847               13003.38
##   R_angular_gyrus_ShapeIndex R_angular_gyrus_Curvedness
## 1                  0.2994884                  0.1106102
## 2                  0.2994884                  0.1106102
## 3                  0.2994884                  0.1106102
## 4                  0.2994884                  0.1106102
## 5                  0.2994884                  0.1106102
## 6                  0.2994884                  0.1106102
##   L_precuneus_AvgMeanCurvature L_precuneus_ComputeArea L_precuneus_Volume
## 1                    0.1026454                3065.234           9302.229
## 2                    0.1026454                3065.234           9302.229
## 3                    0.1026454                3065.234           9302.229
## 4                    0.1026454                3065.234           9302.229
## 5                    0.1026454                3065.234           9302.229
## 6                    0.1026454                3065.234           9302.229
##   L_precuneus_ShapeIndex L_precuneus_Curvedness
## 1              0.3086211              0.0969586
## 2              0.3086211              0.0969586
## 3              0.3086211              0.0969586
## 4              0.3086211              0.0969586
## 5              0.3086211              0.0969586
## 6              0.3086211              0.0969586
##   R_precuneus_AvgMeanCurvature R_precuneus_ComputeArea R_precuneus_Volume
## 1                    0.1078925                3332.431            11293.9
## 2                    0.1078925                3332.431            11293.9
## 3                    0.1078925                3332.431            11293.9
## 4                    0.1078925                3332.431            11293.9
## 5                    0.1078925                3332.431            11293.9
## 6                    0.1078925                3332.431            11293.9
##   R_precuneus_ShapeIndex R_precuneus_Curvedness
## 1              0.3032337             0.09921845
## 2              0.3032337             0.09921845
## 3              0.3032337             0.09921845
## 4              0.3032337             0.09921845
## 5              0.3032337             0.09921845
## 6              0.3032337             0.09921845
##   L_superior_occipital_gyrus_AvgMeanCurvature
## 1                                    0.120578
## 2                                    0.120578
## 3                                    0.120578
## 4                                    0.120578
## 5                                    0.120578
## 6                                    0.120578
##   L_superior_occipital_gyrus_ComputeArea L_superior_occipital_gyrus_Volume
## 1                               1909.412                          5150.974
## 2                               1909.412                          5150.974
## 3                               1909.412                          5150.974
## 4                               1909.412                          5150.974
## 5                               1909.412                          5150.974
## 6                               1909.412                          5150.974
##   L_superior_occipital_gyrus_ShapeIndex
## 1                              0.271993
## 2                              0.271993
## 3                              0.271993
## 4                              0.271993
## 5                              0.271993
## 6                              0.271993
##   L_superior_occipital_gyrus_Curvedness
## 1                             0.1500819
## 2                             0.1500819
## 3                             0.1500819
## 4                             0.1500819
## 5                             0.1500819
## 6                             0.1500819
##   R_superior_occipital_gyrus_AvgMeanCurvature
## 1                                   0.1171069
## 2                                   0.1171069
## 3                                   0.1171069
## 4                                   0.1171069
## 5                                   0.1171069
## 6                                   0.1171069
##   R_superior_occipital_gyrus_ComputeArea R_superior_occipital_gyrus_Volume
## 1                               2173.619                          6231.256
## 2                               2173.619                          6231.256
## 3                               2173.619                          6231.256
## 4                               2173.619                          6231.256
## 5                               2173.619                          6231.256
## 6                               2173.619                          6231.256
##   R_superior_occipital_gyrus_ShapeIndex
## 1                             0.2585772
## 2                             0.2585772
## 3                             0.2585772
## 4                             0.2585772
## 5                             0.2585772
## 6                             0.2585772
##   R_superior_occipital_gyrus_Curvedness
## 1                             0.1520477
## 2                             0.1520477
## 3                             0.1520477
## 4                             0.1520477
## 5                             0.1520477
## 6                             0.1520477
##   L_middle_occipital_gyrus_AvgMeanCurvature
## 1                                0.08442675
## 2                                0.08442675
## 3                                0.08442675
## 4                                0.08442675
## 5                                0.08442675
## 6                                0.08442675
##   L_middle_occipital_gyrus_ComputeArea L_middle_occipital_gyrus_Volume
## 1                             4503.611                        17128.71
## 2                             4503.611                        17128.71
## 3                             4503.611                        17128.71
## 4                             4503.611                        17128.71
## 5                             4503.611                        17128.71
## 6                             4503.611                        17128.71
##   L_middle_occipital_gyrus_ShapeIndex L_middle_occipital_gyrus_Curvedness
## 1                           0.3417904                          0.08082197
## 2                           0.3417904                          0.08082197
## 3                           0.3417904                          0.08082197
## 4                           0.3417904                          0.08082197
## 5                           0.3417904                          0.08082197
## 6                           0.3417904                          0.08082197
##   R_middle_occipital_gyrus_AvgMeanCurvature
## 1                                0.09667509
## 2                                0.09667509
## 3                                0.09667509
## 4                                0.09667509
## 5                                0.09667509
## 6                                0.09667509
##   R_middle_occipital_gyrus_ComputeArea R_middle_occipital_gyrus_Volume
## 1                             5311.343                        20127.27
## 2                             5311.343                        20127.27
## 3                             5311.343                        20127.27
## 4                             5311.343                        20127.27
## 5                             5311.343                        20127.27
## 6                             5311.343                        20127.27
##   R_middle_occipital_gyrus_ShapeIndex R_middle_occipital_gyrus_Curvedness
## 1                           0.3181087                          0.08639906
## 2                           0.3181087                          0.08639906
## 3                           0.3181087                          0.08639906
## 4                           0.3181087                          0.08639906
## 5                           0.3181087                          0.08639906
## 6                           0.3181087                          0.08639906
##   L_inferior_occipital_gyrus_AvgMeanCurvature
## 1                                   0.1102742
## 2                                   0.1102742
## 3                                   0.1102742
## 4                                   0.1102742
## 5                                   0.1102742
## 6                                   0.1102742
##   L_inferior_occipital_gyrus_ComputeArea L_inferior_occipital_gyrus_Volume
## 1                               2575.385                          7956.538
## 2                               2575.385                          7956.538
## 3                               2575.385                          7956.538
## 4                               2575.385                          7956.538
## 5                               2575.385                          7956.538
## 6                               2575.385                          7956.538
##   L_inferior_occipital_gyrus_ShapeIndex
## 1                             0.3179899
## 2                             0.3179899
## 3                             0.3179899
## 4                             0.3179899
## 5                             0.3179899
## 6                             0.3179899
##   L_inferior_occipital_gyrus_Curvedness
## 1                             0.1061467
## 2                             0.1061467
## 3                             0.1061467
## 4                             0.1061467
## 5                             0.1061467
## 6                             0.1061467
##   R_inferior_occipital_gyrus_AvgMeanCurvature
## 1                                  0.08905351
## 2                                  0.08905351
## 3                                  0.08905351
## 4                                  0.08905351
## 5                                  0.08905351
## 6                                  0.08905351
##   R_inferior_occipital_gyrus_ComputeArea R_inferior_occipital_gyrus_Volume
## 1                                3322.39                          12708.51
## 2                                3322.39                          12708.51
## 3                                3322.39                          12708.51
## 4                                3322.39                          12708.51
## 5                                3322.39                          12708.51
## 6                                3322.39                          12708.51
##   R_inferior_occipital_gyrus_ShapeIndex
## 1                             0.3491609
## 2                             0.3491609
## 3                             0.3491609
## 4                             0.3491609
## 5                             0.3491609
## 6                             0.3491609
##   R_inferior_occipital_gyrus_Curvedness L_cuneus_AvgMeanCurvature
## 1                             0.0768138                 0.1215609
## 2                             0.0768138                 0.1215609
## 3                             0.0768138                 0.1215609
## 4                             0.0768138                 0.1215609
## 5                             0.0768138                 0.1215609
## 6                             0.0768138                 0.1215609
##   L_cuneus_ComputeArea L_cuneus_Volume L_cuneus_ShapeIndex
## 1             2430.494        6097.885            0.300488
## 2             2430.494        6097.885            0.300488
## 3             2430.494        6097.885            0.300488
## 4             2430.494        6097.885            0.300488
## 5             2430.494        6097.885            0.300488
## 6             2430.494        6097.885            0.300488
##   L_cuneus_Curvedness R_cuneus_AvgMeanCurvature R_cuneus_ComputeArea
## 1           0.1215284                 0.1052953             2722.789
## 2           0.1215284                 0.1052953             2722.789
## 3           0.1215284                 0.1052953             2722.789
## 4           0.1215284                 0.1052953             2722.789
## 5           0.1215284                 0.1052953             2722.789
## 6           0.1215284                 0.1052953             2722.789
##   R_cuneus_Volume R_cuneus_ShapeIndex R_cuneus_Curvedness
## 1        8342.228           0.2938111           0.1017114
## 2        8342.228           0.2938111           0.1017114
## 3        8342.228           0.2938111           0.1017114
## 4        8342.228           0.2938111           0.1017114
## 5        8342.228           0.2938111           0.1017114
## 6        8342.228           0.2938111           0.1017114
##   L_superior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.08818216
## 2                                 0.08818216
## 3                                 0.08818216
## 4                                 0.08818216
## 5                                 0.08818216
## 6                                 0.08818216
##   L_superior_temporal_gyrus_ComputeArea L_superior_temporal_gyrus_Volume
## 1                              7677.646                         32329.76
## 2                              7677.646                         32329.76
## 3                              7677.646                         32329.76
## 4                              7677.646                         32329.76
## 5                              7677.646                         32329.76
## 6                              7677.646                         32329.76
##   L_superior_temporal_gyrus_ShapeIndex
## 1                            0.3832396
## 2                            0.3832396
## 3                            0.3832396
## 4                            0.3832396
## 5                            0.3832396
## 6                            0.3832396
##   L_superior_temporal_gyrus_Curvedness
## 1                           0.06207907
## 2                           0.06207907
## 3                           0.06207907
## 4                           0.06207907
## 5                           0.06207907
## 6                           0.06207907
##   R_superior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.08121426
## 2                                 0.08121426
## 3                                 0.08121426
## 4                                 0.08121426
## 5                                 0.08121426
## 6                                 0.08121426
##   R_superior_temporal_gyrus_ComputeArea R_superior_temporal_gyrus_Volume
## 1                              6343.222                          26888.9
## 2                              6343.222                          26888.9
## 3                              6343.222                          26888.9
## 4                              6343.222                          26888.9
## 5                              6343.222                          26888.9
## 6                              6343.222                          26888.9
##   R_superior_temporal_gyrus_ShapeIndex
## 1                            0.3733774
## 2                            0.3733774
## 3                            0.3733774
## 4                            0.3733774
## 5                            0.3733774
## 6                            0.3733774
##   R_superior_temporal_gyrus_Curvedness
## 1                           0.06523898
## 2                           0.06523898
## 3                           0.06523898
## 4                           0.06523898
## 5                           0.06523898
## 6                           0.06523898
##   L_middle_temporal_gyrus_AvgMeanCurvature
## 1                                0.1057315
## 2                                0.1057315
## 3                                0.1057315
## 4                                0.1057315
## 5                                0.1057315
## 6                                0.1057315
##   L_middle_temporal_gyrus_ComputeArea L_middle_temporal_gyrus_Volume
## 1                            5470.255                       17208.84
## 2                            5470.255                       17208.84
## 3                            5470.255                       17208.84
## 4                            5470.255                       17208.84
## 5                            5470.255                       17208.84
## 6                            5470.255                       17208.84
##   L_middle_temporal_gyrus_ShapeIndex L_middle_temporal_gyrus_Curvedness
## 1                          0.3291948                         0.08871739
## 2                          0.3291948                         0.08871739
## 3                          0.3291948                         0.08871739
## 4                          0.3291948                         0.08871739
## 5                          0.3291948                         0.08871739
## 6                          0.3291948                         0.08871739
##   R_middle_temporal_gyrus_AvgMeanCurvature
## 1                               0.09784834
## 2                               0.09784834
## 3                               0.09784834
## 4                               0.09784834
## 5                               0.09784834
## 6                               0.09784834
##   R_middle_temporal_gyrus_ComputeArea R_middle_temporal_gyrus_Volume
## 1                            6960.965                       27476.33
## 2                            6960.965                       27476.33
## 3                            6960.965                       27476.33
## 4                            6960.965                       27476.33
## 5                            6960.965                       27476.33
## 6                            6960.965                       27476.33
##   R_middle_temporal_gyrus_ShapeIndex R_middle_temporal_gyrus_Curvedness
## 1                          0.3180938                         0.07262339
## 2                          0.3180938                         0.07262339
## 3                          0.3180938                         0.07262339
## 4                          0.3180938                         0.07262339
## 5                          0.3180938                         0.07262339
## 6                          0.3180938                         0.07262339
##   L_inferior_temporal_gyrus_AvgMeanCurvature
## 1                                 0.08440291
## 2                                 0.08440291
## 3                                 0.08440291
## 4                                 0.08440291
## 5                                 0.08440291
## 6                                 0.08440291
##   L_inferior_temporal_gyrus_ComputeArea L_inferior_temporal_gyrus_Volume
## 1                              5925.988                          24980.9
## 2                              5925.988                          24980.9
## 3                              5925.988                          24980.9
## 4                              5925.988                          24980.9
## 5                              5925.988                          24980.9
## 6                              5925.988                          24980.9
##   L_inferior_temporal_gyrus_ShapeIndex
## 1                              0.38634
## 2                              0.38634
## 3                              0.38634
## 4                              0.38634
## 5                              0.38634
## 6                              0.38634
##   L_inferior_temporal_gyrus_Curvedness
## 1                           0.06998834
## 2                           0.06998834
## 3                           0.06998834
## 4                           0.06998834
## 5                           0.06998834
## 6                           0.06998834
##   R_inferior_temporal_gyrus_AvgMeanCurvature
## 1                                  0.1430986
## 2                                  0.1430986
## 3                                  0.1430986
## 4                                  0.1430986
## 5                                  0.1430986
## 6                                  0.1430986
##   R_inferior_temporal_gyrus_ComputeArea R_inferior_temporal_gyrus_Volume
## 1                              5113.919                         18076.97
## 2                              5113.919                         18076.97
## 3                              5113.919                         18076.97
## 4                              5113.919                         18076.97
## 5                              5113.919                         18076.97
## 6                              5113.919                         18076.97
##   R_inferior_temporal_gyrus_ShapeIndex
## 1                            0.3730978
## 2                            0.3730978
## 3                            0.3730978
## 4                            0.3730978
## 5                            0.3730978
## 6                            0.3730978
##   R_inferior_temporal_gyrus_Curvedness
## 1                           0.09922728
## 2                           0.09922728
## 3                           0.09922728
## 4                           0.09922728
## 5                           0.09922728
## 6                           0.09922728
##   L_parahippocampal_gyrus_AvgMeanCurvature
## 1                                0.1077122
## 2                                0.1077122
## 3                                0.1077122
## 4                                0.1077122
## 5                                0.1077122
## 6                                0.1077122
##   L_parahippocampal_gyrus_ComputeArea L_parahippocampal_gyrus_Volume
## 1                            2844.754                       7480.951
## 2                            2844.754                       7480.951
## 3                            2844.754                       7480.951
## 4                            2844.754                       7480.951
## 5                            2844.754                       7480.951
## 6                            2844.754                       7480.951
##   L_parahippocampal_gyrus_ShapeIndex L_parahippocampal_gyrus_Curvedness
## 1                          0.2607401                          0.1022136
## 2                          0.2607401                          0.1022136
## 3                          0.2607401                          0.1022136
## 4                          0.2607401                          0.1022136
## 5                          0.2607401                          0.1022136
## 6                          0.2607401                          0.1022136
##   R_parahippocampal_gyrus_AvgMeanCurvature
## 1                                0.1026529
## 2                                0.1026529
## 3                                0.1026529
## 4                                0.1026529
## 5                                0.1026529
## 6                                0.1026529
##   R_parahippocampal_gyrus_ComputeArea R_parahippocampal_gyrus_Volume
## 1                            3198.464                       9512.674
## 2                            3198.464                       9512.674
## 3                            3198.464                       9512.674
## 4                            3198.464                       9512.674
## 5                            3198.464                       9512.674
## 6                            3198.464                       9512.674
##   R_parahippocampal_gyrus_ShapeIndex R_parahippocampal_gyrus_Curvedness
## 1                          0.3130394                         0.09406152
## 2                          0.3130394                         0.09406152
## 3                          0.3130394                         0.09406152
## 4                          0.3130394                         0.09406152
## 5                          0.3130394                         0.09406152
## 6                          0.3130394                         0.09406152
##   L_lingual_gyrus_AvgMeanCurvature L_lingual_gyrus_ComputeArea
## 1                       0.09506937                    3990.686
## 2                       0.09506937                    3990.686
## 3                       0.09506937                    3990.686
## 4                       0.09506937                    3990.686
## 5                       0.09506937                    3990.686
## 6                       0.09506937                    3990.686
##   L_lingual_gyrus_Volume L_lingual_gyrus_ShapeIndex
## 1               15329.18                  0.3268375
## 2               15329.18                  0.3268375
## 3               15329.18                  0.3268375
## 4               15329.18                  0.3268375
## 5               15329.18                  0.3268375
## 6               15329.18                  0.3268375
##   L_lingual_gyrus_Curvedness R_lingual_gyrus_AvgMeanCurvature
## 1                 0.08228135                       0.08600172
## 2                 0.08228135                       0.08600172
## 3                 0.08228135                       0.08600172
## 4                 0.08228135                       0.08600172
## 5                 0.08228135                       0.08600172
## 6                 0.08228135                       0.08600172
##   R_lingual_gyrus_ComputeArea R_lingual_gyrus_Volume
## 1                    4208.788                16959.6
## 2                    4208.788                16959.6
## 3                    4208.788                16959.6
## 4                    4208.788                16959.6
## 5                    4208.788                16959.6
## 6                    4208.788                16959.6
##   R_lingual_gyrus_ShapeIndex R_lingual_gyrus_Curvedness
## 1                   0.320331                 0.07572543
## 2                   0.320331                 0.07572543
## 3                   0.320331                 0.07572543
## 4                   0.320331                 0.07572543
## 5                   0.320331                 0.07572543
## 6                   0.320331                 0.07572543
##   L_fusiform_gyrus_AvgMeanCurvature L_fusiform_gyrus_ComputeArea
## 1                         0.1038532                     4534.707
## 2                         0.1038532                     4534.707
## 3                         0.1038532                     4534.707
## 4                         0.1038532                     4534.707
## 5                         0.1038532                     4534.707
## 6                         0.1038532                     4534.707
##   L_fusiform_gyrus_Volume L_fusiform_gyrus_ShapeIndex
## 1                15830.32                   0.3102792
## 2                15830.32                   0.3102792
## 3                15830.32                   0.3102792
## 4                15830.32                   0.3102792
## 5                15830.32                   0.3102792
## 6                15830.32                   0.3102792
##   L_fusiform_gyrus_Curvedness R_fusiform_gyrus_AvgMeanCurvature
## 1                  0.08341972                         0.1063175
## 2                  0.08341972                         0.1063175
## 3                  0.08341972                         0.1063175
## 4                  0.08341972                         0.1063175
## 5                  0.08341972                         0.1063175
## 6                  0.08341972                         0.1063175
##   R_fusiform_gyrus_ComputeArea R_fusiform_gyrus_Volume
## 1                     3945.037                14471.84
## 2                     3945.037                14471.84
## 3                     3945.037                14471.84
## 4                     3945.037                14471.84
## 5                     3945.037                14471.84
## 6                     3945.037                14471.84
##   R_fusiform_gyrus_ShapeIndex R_fusiform_gyrus_Curvedness Sex Weight
## 1                   0.3592094                   0.0776228   1   74.2
## 2                   0.3592094                   0.0776228   1   74.2
## 3                   0.3592094                   0.0776228   1   74.2
## 4                   0.3592094                   0.0776228   1   74.2
## 5                   0.3592094                   0.0776228   1   74.2
## 6                   0.3592094                   0.0776228   1   74.2
##   ResearchGroup VisitID     Age chr12_rs34637584_GT chr12_rs34637584_DP
## 1            PD       1 65.1808                   0                  23
## 2            PD       1 65.1808                   0                  23
## 3            PD       1 65.1808                   0                  23
## 4            PD       1 65.1808                   0                  23
## 5            PD       1 65.1808                   0                  23
## 6            PD       1 65.1808                   0                  23
##   chr12_rs34637584_GQ chr17_rs11868035_GT chr17_rs11868035_DP
## 1                  69                   1                  53
## 2                  69                   1                  53
## 3                  69                   1                  53
## 4                  69                   1                  53
## 5                  69                   1                  53
## 6                  69                   1                  53
##   chr17_rs11868035_GQ chr17_rs11012_GT chr17_rs11012_DP chr17_rs11012_GQ
## 1                  99                1               60               99
## 2                  99                1               60               99
## 3                  99                1               60               99
## 4                  99                1               60               99
## 5                  99                1               60               99
## 6                  99                1               60               99
##   chr17_rs393152_GT chr17_rs393152_DP chr17_rs393152_GQ
## 1                 1                15                99
## 2                 1                15                99
## 3                 1                15                99
## 4                 1                15                99
## 5                 1                15                99
## 6                 1                15                99
##   chr17_rs12185268_GT chr17_rs12185268_DP chr17_rs12185268_GQ
## 1                   1                  65                  99
## 2                   1                  65                  99
## 3                   1                  65                  99
## 4                   1                  65                  99
## 5                   1                  65                  99
## 6                   1                  65                  99
##   chr17_rs199533_GT chr17_rs199533_DP chr17_rs199533_GQ
## 1                 0                20                60
## 2                 0                20                60
## 3                 0                20                60
## 4                 0                20                60
## 5                 0                20                60
## 6                 0                20                60
##   chr12_rs34637584_AD_1 chr12_rs34637584_AD_2 chr17_rs11868035_AD_1
## 1                    23                     0                    32
## 2                    23                     0                    32
## 3                    23                     0                    32
## 4                    23                     0                    32
## 5                    23                     0                    32
## 6                    23                     0                    32
##   chr17_rs11868035_AD_2 chr17_rs11012_AD_1 chr17_rs11012_AD_2
## 1                    21                 32                 28
## 2                    21                 32                 28
## 3                    21                 32                 28
## 4                    21                 32                 28
## 5                    21                 32                 28
## 6                    21                 32                 28
##   chr17_rs393152_AD_1 chr17_rs393152_AD_2 chr17_rs12185268_AD_1
## 1                  10                   5                    27
## 2                  10                   5                    27
## 3                  10                   5                    27
## 4                  10                   5                    27
## 5                  10                   5                    27
## 6                  10                   5                    27
##   chr17_rs12185268_AD_2 chr17_rs199533_AD_1 chr17_rs199533_AD_2
## 1                    38                  20                   0
## 2                    38                  20                   0
## 3                    38                  20                   0
## 4                    38                  20                   0
## 5                    38                  20                   0
## 6                    38                  20                   0
##   chr12_rs34637584_PL_1 chr12_rs34637584_PL_2 chr12_rs34637584_PL_3
## 1                     0                    69                   726
## 2                     0                    69                   726
## 3                     0                    69                   726
## 4                     0                    69                   726
## 5                     0                    69                   726
## 6                     0                    69                   726
##   chr17_rs11868035_PL_1 chr17_rs11868035_PL_2 chr17_rs11868035_PL_3
## 1                   498                     0                   848
## 2                   498                     0                   848
## 3                   498                     0                   848
## 4                   498                     0                   848
## 5                   498                     0                   848
## 6                   498                     0                   848
##   chr17_rs11012_PL_1 chr17_rs11012_PL_2 chr17_rs11012_PL_3
## 1                679                  0                735
## 2                679                  0                735
## 3                679                  0                735
## 4                679                  0                735
## 5                679                  0                735
## 6                679                  0                735
##   chr17_rs393152_PL_1 chr17_rs393152_PL_2 chr17_rs393152_PL_3
## 1                 140                   0                 242
## 2                 140                   0                 242
## 3                 140                   0                 242
## 4                 140                   0                 242
## 5                 140                   0                 242
## 6                 140                   0                 242
##   chr17_rs12185268_PL_1 chr17_rs12185268_PL_2 chr17_rs12185268_PL_3
## 1                  1013                     0                   616
## 2                  1013                     0                   616
## 3                  1013                     0                   616
## 4                  1013                     0                   616
## 5                  1013                     0                   616
## 6                  1013                     0                   616
##   chr17_rs199533_PL_1 chr17_rs199533_PL_2 chr17_rs199533_PL_3 UPDRS_part_I
## 1                   0                  60                 709            0
## 2                   0                  60                 709           NA
## 3                   0                  60                 709            1
## 4                   0                  60                 709            0
## 5                   0                  60                 709            1
## 6                   0                  60                 709            4
##   UPDRS_part_II UPDRS_part_III UPDRS_part_IV time_visit PD
## 1             2             12            NA          0  0
## 2            NA             NA            NA         54  0
## 3             4             29            NA         18  0
## 4             2             39            NA         24  0
## 5            11             42             0         42  0
## 6             3             20            NA         12  0
##                   COGSTATE COGDECLN FNCDTCOG    COGDXCL EDUCYRS RAWHITE
## 1 Normal Cognition (PD-NC)       No       No 90% - 100%      16     Yes
## 2 Normal Cognition (PD-NC)       No       No 90% - 100%      16     Yes
## 3 Normal Cognition (PD-NC)       No       No 90% - 100%      16     Yes
## 4 Normal Cognition (PD-NC)       No       No 90% - 100%      16     Yes
## 5 Normal Cognition (PD-NC)       No       No 90% - 100%      16     Yes
## 6 Normal Cognition (PD-NC)       No       No 90% - 100%      16     Yes
##                APPRDX
## 1 Parkinson's disease
## 2 Parkinson's disease
## 3 Parkinson's disease
## 4 Parkinson's disease
## 5 Parkinson's disease
## 6 Parkinson's disease

Longtitudinal analysis with different time points of UPDRS measurements

# use complete dataset with the result
DataMissOm<-na.omit(subset(ppmi_long,select=c(time_visit,PD,FID_IID,COGSTATE,COGDECLN,FNCDTCOG,COGDXCL,EDUCYRS,L_superior_parietal_gyrus_ComputeArea
                                              ,L_superior_parietal_gyrus_Volume,R_superior_parietal_gyrus_ComputeArea,R_superior_parietal_gyrus_Volume,L_putamen_ComputeArea,L_putamen_Volume,R_putamen_Volume 
                                              ,R_putamen_ShapeIndex,L_caudate_ComputeArea,L_caudate_Volume,R_caudate_ComputeArea,R_caudate_Volume,chr12_rs34637584_GT 
                                              ,chr17_rs11868035_GT,chr17_rs11012_GT,chr17_rs393152_GT,chr17_rs12185268_GT,chr17_rs199533_GT,Sex,Weight,Age,UPDRS_part_I,UPDRS_part_II,UPDRS_part_III)))
#normalize continuous variables
for(i in c(8:20,28:32)){
  DataMissOm[,i]<-scale(DataMissOm[,i])
}

library(geepack)
DataMissOm$COGSTATE<-as.numeric(DataMissOm$COGSTATE)
DataMissOm$COGDECLN<-as.numeric(DataMissOm$COGDECLN)
DataMissOm$FNCDTCOG<-as.numeric(DataMissOm$FNCDTCOG)
DataMissOm$COGDXCL<-as.numeric(DataMissOm$COGDXCL)
model_gee_UPDRS<-geeglm(PD~L_superior_parietal_gyrus_ComputeArea
                        +L_superior_parietal_gyrus_Volume+R_superior_parietal_gyrus_ComputeArea+R_superior_parietal_gyrus_Volume+L_putamen_ComputeArea+L_putamen_Volume+R_putamen_Volume 
                        +R_putamen_ShapeIndex+L_caudate_ComputeArea+L_caudate_Volume+R_caudate_ComputeArea+R_caudate_Volume+chr12_rs34637584_GT 
                        +chr17_rs11868035_GT+chr17_rs11012_GT+chr17_rs393152_GT+chr17_rs12185268_GT+chr17_rs199533_GT+Sex+Weight+Age
                        +UPDRS_part_I+UPDRS_part_II+UPDRS_part_III+FID_IID+COGSTATE+COGDECLN+FNCDTCOG+COGDXCL+EDUCYRS,
                        data=DataMissOm,waves=time_visit,family="binomial",id=FID_IID,corstr="exchangeable",scale.fix=TRUE)
summary(model_gee_UPDRS)
## 
## Call:
## geeglm(formula = PD ~ L_superior_parietal_gyrus_ComputeArea + 
##     L_superior_parietal_gyrus_Volume + R_superior_parietal_gyrus_ComputeArea + 
##     R_superior_parietal_gyrus_Volume + L_putamen_ComputeArea + 
##     L_putamen_Volume + R_putamen_Volume + R_putamen_ShapeIndex + 
##     L_caudate_ComputeArea + L_caudate_Volume + R_caudate_ComputeArea + 
##     R_caudate_Volume + chr12_rs34637584_GT + chr17_rs11868035_GT + 
##     chr17_rs11012_GT + chr17_rs393152_GT + chr17_rs12185268_GT + 
##     chr17_rs199533_GT + Sex + Weight + Age + UPDRS_part_I + UPDRS_part_II + 
##     UPDRS_part_III + FID_IID + COGSTATE + COGDECLN + FNCDTCOG + 
##     COGDXCL + EDUCYRS, family = "binomial", data = DataMissOm, 
##     id = FID_IID, waves = time_visit, corstr = "exchangeable", 
##     scale.fix = TRUE)
## 
##  Coefficients:
##                                         Estimate    Std.err     Wald
## (Intercept)                            1.787e+17  6.714e+14 70831.65
## L_superior_parietal_gyrus_ComputeArea -4.700e+17  2.633e+15 31867.29
## L_superior_parietal_gyrus_Volume       5.226e+17  2.836e+15 33961.30
## R_superior_parietal_gyrus_ComputeArea  3.618e+17  1.968e+15 33785.88
## R_superior_parietal_gyrus_Volume      -4.222e+17  2.330e+15 32820.75
## L_putamen_ComputeArea                 -1.330e+17  9.865e+14 18176.48
## L_putamen_Volume                       2.165e+17  1.166e+15 34476.22
## R_putamen_Volume                      -7.282e+16  4.836e+14 22677.60
## R_putamen_ShapeIndex                  -3.817e+15  1.923e+14   393.72
## L_caudate_ComputeArea                 -2.169e+17  1.567e+15 19144.96
## L_caudate_Volume                       1.112e+17  1.159e+15  9199.90
## R_caudate_ComputeArea                  9.570e+16  1.045e+15  8379.14
## R_caudate_Volume                       1.932e+16  7.656e+14   636.44
## chr12_rs34637584_GT                   -1.266e+17  1.230e+15 10595.16
## chr17_rs11868035_GT                    2.584e+16  3.206e+14  6497.19
## chr17_rs11012_GT                       2.435e+15  6.828e+14    12.71
## chr17_rs393152_GT                      1.212e+16  7.579e+14   255.77
## chr17_rs12185268_GT                   -1.241e+17  1.290e+15  9252.73
## chr17_rs199533_GT                      7.307e+16  8.266e+14  7814.16
## Sex                                    5.194e+16  6.038e+14  7398.75
## Weight                                -1.305e+16  2.352e+14  3075.64
## Age                                   -1.208e+16  2.022e+14  3568.28
## UPDRS_part_I                           1.019e+16  1.301e+14  6133.81
## UPDRS_part_II                          2.386e+15  2.648e+14    81.22
## UPDRS_part_III                         5.018e+16  3.686e+14 18537.46
## FID_IID                               -3.435e+13  3.649e+11  8860.45
## COGSTATE                               5.995e+15  2.795e+14   460.15
## COGDECLN                              -2.453e+16  3.557e+14  4753.03
## FNCDTCOG                              -1.571e+17  7.565e+14 43103.79
## COGDXCL                                1.578e+16  6.795e+14   539.41
## EDUCYRS                                3.086e+16  2.071e+14 22193.59
##                                       Pr(>|W|)    
## (Intercept)                            < 2e-16 ***
## L_superior_parietal_gyrus_ComputeArea  < 2e-16 ***
## L_superior_parietal_gyrus_Volume       < 2e-16 ***
## R_superior_parietal_gyrus_ComputeArea  < 2e-16 ***
## R_superior_parietal_gyrus_Volume       < 2e-16 ***
## L_putamen_ComputeArea                  < 2e-16 ***
## L_putamen_Volume                       < 2e-16 ***
## R_putamen_Volume                       < 2e-16 ***
## R_putamen_ShapeIndex                   < 2e-16 ***
## L_caudate_ComputeArea                  < 2e-16 ***
## L_caudate_Volume                       < 2e-16 ***
## R_caudate_ComputeArea                  < 2e-16 ***
## R_caudate_Volume                       < 2e-16 ***
## chr12_rs34637584_GT                    < 2e-16 ***
## chr17_rs11868035_GT                    < 2e-16 ***
## chr17_rs11012_GT                      0.000363 ***
## chr17_rs393152_GT                      < 2e-16 ***
## chr17_rs12185268_GT                    < 2e-16 ***
## chr17_rs199533_GT                      < 2e-16 ***
## Sex                                    < 2e-16 ***
## Weight                                 < 2e-16 ***
## Age                                    < 2e-16 ***
## UPDRS_part_I                           < 2e-16 ***
## UPDRS_part_II                          < 2e-16 ***
## UPDRS_part_III                         < 2e-16 ***
## FID_IID                                < 2e-16 ***
## COGSTATE                               < 2e-16 ***
## COGDECLN                               < 2e-16 ***
## FNCDTCOG                               < 2e-16 ***
## COGDXCL                                < 2e-16 ***
## EDUCYRS                                < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Scale is fixed.
## 
## Correlation: Structure = exchangeable  Link = identity 
## 
## Estimated Correlation Parameters:
##        Estimate   Std.err
## alpha 2.217e+15 1.086e+30
## Number of clusters:   406   Maximum cluster size: 12
library(lme4)
## Loading required package: Matrix
model_lmm_UPDRS<-glmer(PD~L_superior_parietal_gyrus_ComputeArea
                       +L_superior_parietal_gyrus_Volume+R_superior_parietal_gyrus_ComputeArea+R_superior_parietal_gyrus_Volume+L_putamen_ComputeArea+L_putamen_Volume+R_putamen_Volume 
                       +R_putamen_ShapeIndex+L_caudate_ComputeArea+L_caudate_Volume+R_caudate_ComputeArea+R_caudate_Volume+chr12_rs34637584_GT 
                       +chr17_rs11868035_GT+chr17_rs11012_GT+chr17_rs393152_GT+chr17_rs12185268_GT+chr17_rs199533_GT+Sex+Weight+Age+UPDRS_part_I+UPDRS_part_II+UPDRS_part_III+FID_IID+COGSTATE+COGDECLN+FNCDTCOG+COGDXCL+EDUCYRS
                       +(1|FID_IID),control = glmerControl(optCtrl=list(maxfun=20000)),
                       data=DataMissOm,family="binomial")
summary(model_lmm_UPDRS)
## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: binomial  ( logit )
## Formula: 
## PD ~ L_superior_parietal_gyrus_ComputeArea + L_superior_parietal_gyrus_Volume +  
##     R_superior_parietal_gyrus_ComputeArea + R_superior_parietal_gyrus_Volume +  
##     L_putamen_ComputeArea + L_putamen_Volume + R_putamen_Volume +  
##     R_putamen_ShapeIndex + L_caudate_ComputeArea + L_caudate_Volume +  
##     R_caudate_ComputeArea + R_caudate_Volume + chr12_rs34637584_GT +  
##     chr17_rs11868035_GT + chr17_rs11012_GT + chr17_rs393152_GT +  
##     chr17_rs12185268_GT + chr17_rs199533_GT + Sex + Weight +  
##     Age + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + FID_IID +  
##     COGSTATE + COGDECLN + FNCDTCOG + COGDXCL + EDUCYRS + (1 |  
##     FID_IID)
##    Data: DataMissOm
## Control: glmerControl(optCtrl = list(maxfun = 20000))
## 
##      AIC      BIC   logLik deviance df.resid 
##    193.8    380.9    -64.9    129.8     2530 
## 
## Scaled residuals: 
##    Min     1Q Median     3Q    Max 
## -0.682  0.000  0.000  0.000  0.706 
## 
## Random effects:
##  Groups  Name        Variance Std.Dev.
##  FID_IID (Intercept) 36.3     6.03    
## Number of obs: 2562, groups:  FID_IID, 406
## 
## Fixed effects:
##                                        Estimate Std. Error z value
## (Intercept)                           -7.82e+01   6.52e+04    0.00
## L_superior_parietal_gyrus_ComputeArea -1.94e+00   6.84e+00   -0.28
## L_superior_parietal_gyrus_Volume       2.34e+00   7.22e+00    0.32
## R_superior_parietal_gyrus_ComputeArea -1.36e-01   6.28e+00   -0.02
## R_superior_parietal_gyrus_Volume       1.31e+00   6.66e+00    0.20
## L_putamen_ComputeArea                 -3.63e+00   5.75e+00   -0.63
## L_putamen_Volume                       2.84e+00   5.15e+00    0.55
## R_putamen_Volume                      -2.95e-01   3.41e+00   -0.09
## R_putamen_ShapeIndex                  -2.06e-01   1.35e+00   -0.15
## L_caudate_ComputeArea                 -6.77e+00   7.93e+00   -0.85
## L_caudate_Volume                       3.38e+00   7.58e+00    0.45
## R_caudate_ComputeArea                  5.30e+00   8.53e+00    0.62
## R_caudate_Volume                      -2.08e+00   7.78e+00   -0.27
## chr12_rs34637584_GT                   -4.51e+00   4.94e+02   -0.01
## chr17_rs11868035_GT                   -4.92e-01   1.65e+00   -0.30
## chr17_rs11012_GT                       7.34e-01   3.40e+00    0.22
## chr17_rs393152_GT                      2.92e+00   3.43e+00    0.85
## chr17_rs12185268_GT                    3.02e+00   5.76e+00    0.52
## chr17_rs199533_GT                     -2.90e+00   4.92e+00   -0.59
## Sex                                    1.09e+00   2.73e+00    0.40
## Weight                                 1.88e+00   1.35e+00    1.40
## Age                                    1.83e+00   1.33e+00    1.38
## UPDRS_part_I                           3.29e-01   1.70e+00    0.19
## UPDRS_part_II                         -1.28e+01   4.02e+00   -3.19
## UPDRS_part_III                        -2.09e+01   5.74e+00   -3.65
## FID_IID                               -1.60e-03   3.31e-03   -0.48
## COGSTATE                               9.42e+00   8.01e+00    1.18
## COGDECLN                              -4.48e+00   4.12e+00   -1.09
## FNCDTCOG                               8.71e+00   6.52e+04    0.00
## COGDXCL                               -4.27e+00   5.06e+00   -0.84
## EDUCYRS                                3.68e-02   1.29e+00    0.03
##                                       Pr(>|z|)    
## (Intercept)                            0.99904    
## L_superior_parietal_gyrus_ComputeArea  0.77698    
## L_superior_parietal_gyrus_Volume       0.74594    
## R_superior_parietal_gyrus_ComputeArea  0.98267    
## R_superior_parietal_gyrus_Volume       0.84431    
## L_putamen_ComputeArea                  0.52797    
## L_putamen_Volume                       0.58167    
## R_putamen_Volume                       0.93113    
## R_putamen_ShapeIndex                   0.87846    
## L_caudate_ComputeArea                  0.39352    
## L_caudate_Volume                       0.65557    
## R_caudate_ComputeArea                  0.53451    
## R_caudate_Volume                       0.78918    
## chr12_rs34637584_GT                    0.99272    
## chr17_rs11868035_GT                    0.76636    
## chr17_rs11012_GT                       0.82913    
## chr17_rs393152_GT                      0.39461    
## chr17_rs12185268_GT                    0.60026    
## chr17_rs199533_GT                      0.55589    
## Sex                                    0.68982    
## Weight                                 0.16203    
## Age                                    0.16687    
## UPDRS_part_I                           0.84611    
## UPDRS_part_II                          0.00140 ** 
## UPDRS_part_III                         0.00026 ***
## FID_IID                                0.62892    
## COGSTATE                               0.23984    
## COGDECLN                               0.27759    
## FNCDTCOG                               0.99989    
## COGDXCL                                0.39832    
## EDUCYRS                                0.97715    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation matrix not shown by default, as p = 31 > 12.
## Use print(x, correlation=TRUE)  or
##   vcov(x)     if you need it
## fit warnings:
## Some predictor variables are on very different scales: consider rescaling
## convergence code: 0
## unable to evaluate scaled gradient
## Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
## failure to converge in 20000 evaluations
length(unique(DataMissOm$FID_IID)) #406 patients
## [1] 406
nrow(DataMissOm) #2562 observations
## [1] 2562

Longtitudinal analysis with different time point of brain imaging measures

ppmi_base<-read.csv("ppmi_ROI_baseline.csv",header=TRUE)
ppmi_base<-ppmi_base[,c(2,24:26,29:33)] #may add 27 28
ppmi_new<-read.csv("PPMI_GSA_clinical.csv",header=TRUE)
ppmi_imaging<-ppmi_new[,1:335]

merged_dataset<-merge(ppmi_imaging,ppmi_base,by="FID_IID",all.x=TRUE)
DataMissOm<-na.omit(subset(merged_dataset,select=c(VisitID,ResearchGroup,FID_IID,COGSTATE,COGDECLN,FNCDTCOG,COGDXCL,EDUCYRS,L_superior_parietal_gyrus_ComputeArea
                                                   ,L_superior_parietal_gyrus_Volume,R_superior_parietal_gyrus_ComputeArea,R_superior_parietal_gyrus_Volume,L_putamen_ComputeArea,L_putamen_Volume,R_putamen_Volume 
                                                   ,R_putamen_ShapeIndex,L_caudate_ComputeArea,L_caudate_Volume,R_caudate_ComputeArea,R_caudate_Volume,chr12_rs34637584_GT 
                                                   ,chr17_rs11868035_GT,chr17_rs11012_GT,chr17_rs393152_GT,chr17_rs12185268_GT,chr17_rs199533_GT,Sex,Weight,Age,UPDRS_Part_I_Summary_Score_Baseline,UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline,UPDRS_Part_III_Summary_Score_Baseline)))
#normalize continuous variables
for(i in c(9:20,28:32)){
  DataMissOm[,i]<-scale(DataMissOm[,i])
}
library(geepack)
DataMissOm$COGSTATE<-as.numeric(DataMissOm$COGSTATE)
DataMissOm$COGDECLN<-as.numeric(DataMissOm$COGDECLN)
DataMissOm$FNCDTCOG<-as.numeric(DataMissOm$FNCDTCOG)
DataMissOm$COGDXCL<-as.numeric(DataMissOm$COGDXCL)
DataMissOm$PD<-ifelse(DataMissOm$ResearchGroup=="Control",0,1)
model_gee_imaging<-geeglm(PD~L_superior_parietal_gyrus_ComputeArea
                          +L_superior_parietal_gyrus_Volume+R_superior_parietal_gyrus_ComputeArea+R_superior_parietal_gyrus_Volume+L_putamen_ComputeArea+L_putamen_Volume+R_putamen_Volume 
                          +R_putamen_ShapeIndex+L_caudate_ComputeArea+L_caudate_Volume+R_caudate_ComputeArea+R_caudate_Volume+chr12_rs34637584_GT 
                          +chr17_rs11868035_GT+chr17_rs11012_GT+chr17_rs393152_GT+chr17_rs12185268_GT+chr17_rs199533_GT+Sex+Weight+Age
                          +UPDRS_Part_I_Summary_Score_Baseline+UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline+UPDRS_Part_III_Summary_Score_Baseline+FID_IID+COGSTATE+COGDECLN+FNCDTCOG+COGDXCL+EDUCYRS,
                          data=DataMissOm,waves=VisitID,family="binomial",id=FID_IID,corstr="exchangeable",scale.fix=TRUE)
summary(model_gee_imaging)
## 
## Call:
## geeglm(formula = PD ~ L_superior_parietal_gyrus_ComputeArea + 
##     L_superior_parietal_gyrus_Volume + R_superior_parietal_gyrus_ComputeArea + 
##     R_superior_parietal_gyrus_Volume + L_putamen_ComputeArea + 
##     L_putamen_Volume + R_putamen_Volume + R_putamen_ShapeIndex + 
##     L_caudate_ComputeArea + L_caudate_Volume + R_caudate_ComputeArea + 
##     R_caudate_Volume + chr12_rs34637584_GT + chr17_rs11868035_GT + 
##     chr17_rs11012_GT + chr17_rs393152_GT + chr17_rs12185268_GT + 
##     chr17_rs199533_GT + Sex + Weight + Age + UPDRS_Part_I_Summary_Score_Baseline + 
##     UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline + 
##     UPDRS_Part_III_Summary_Score_Baseline + FID_IID + COGSTATE + 
##     COGDECLN + FNCDTCOG + COGDXCL + EDUCYRS, family = "binomial", 
##     data = DataMissOm, id = FID_IID, waves = VisitID, corstr = "exchangeable", 
##     scale.fix = TRUE)
## 
##  Coefficients:
##                                                             Estimate
## (Intercept)                                                10.421512
## L_superior_parietal_gyrus_ComputeArea                       0.751061
## L_superior_parietal_gyrus_Volume                           -1.251801
## R_superior_parietal_gyrus_ComputeArea                       0.689802
## R_superior_parietal_gyrus_Volume                           -0.356608
## L_putamen_ComputeArea                                       0.926960
## L_putamen_Volume                                           -0.609840
## R_putamen_Volume                                           -0.077577
## R_putamen_ShapeIndex                                        0.256049
## L_caudate_ComputeArea                                       0.139422
## L_caudate_Volume                                            0.437466
## R_caudate_ComputeArea                                       0.009620
## R_caudate_Volume                                           -0.681865
## chr12_rs34637584_GT                                        48.038347
## chr17_rs11868035_GT                                        -0.109276
## chr17_rs11012_GT                                           -0.252672
## chr17_rs393152_GT                                          -0.998842
## chr17_rs12185268_GT                                         0.760646
## chr17_rs199533_GT                                          -0.040611
## Sex                                                         0.436308
## Weight                                                     -0.005619
## Age                                                        -0.493743
## UPDRS_Part_I_Summary_Score_Baseline                        -0.399624
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline  0.994330
## UPDRS_Part_III_Summary_Score_Baseline                       4.581105
## FID_IID                                                     0.000511
## COGSTATE                                                   -2.959439
## COGDECLN                                                   -0.127457
## FNCDTCOG                                                   -0.758775
## COGDXCL                                                     0.710111
## EDUCYRS                                                    -0.042825
##                                                              Std.err  Wald
## (Intercept)                                                 3.640233  8.20
## L_superior_parietal_gyrus_ComputeArea                       0.667863  1.26
## L_superior_parietal_gyrus_Volume                            0.709685  3.11
## R_superior_parietal_gyrus_ComputeArea                       0.685233  1.01
## R_superior_parietal_gyrus_Volume                            0.741701  0.23
## L_putamen_ComputeArea                                       0.797878  1.35
## L_putamen_Volume                                            0.778800  0.61
## R_putamen_Volume                                            0.387239  0.04
## R_putamen_ShapeIndex                                        0.158337  2.62
## L_caudate_ComputeArea                                       0.796874  0.03
## L_caudate_Volume                                            0.768952  0.32
## R_caudate_ComputeArea                                       0.698348  0.00
## R_caudate_Volume                                            0.755324  0.81
## chr12_rs34637584_GT                                               NA    NA
## chr17_rs11868035_GT                                         0.260319  0.18
## chr17_rs11012_GT                                            0.437211  0.33
## chr17_rs393152_GT                                           0.480575  4.32
## chr17_rs12185268_GT                                         0.887839  0.73
## chr17_rs199533_GT                                           0.758373  0.00
## Sex                                                         0.420170  1.08
## Weight                                                      0.182701  0.00
## Age                                                         0.209700  5.54
## UPDRS_Part_I_Summary_Score_Baseline                         0.359180  1.24
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline  0.997760  0.99
## UPDRS_Part_III_Summary_Score_Baseline                       1.528156  8.99
## FID_IID                                                     0.000570  0.80
## COGSTATE                                                    0.842112 12.35
## COGDECLN                                                    0.819498  0.02
## FNCDTCOG                                                    1.175771  0.42
## COGDXCL                                                     0.691705  1.05
## EDUCYRS                                                     0.075770  0.32
##                                                            Pr(>|W|)    
## (Intercept)                                                 0.00420 ** 
## L_superior_parietal_gyrus_ComputeArea                       0.26077    
## L_superior_parietal_gyrus_Volume                            0.07775 .  
## R_superior_parietal_gyrus_ComputeArea                       0.31409    
## R_superior_parietal_gyrus_Volume                            0.63066    
## L_putamen_ComputeArea                                       0.24532    
## L_putamen_Volume                                            0.43360    
## R_putamen_Volume                                            0.84122    
## R_putamen_ShapeIndex                                        0.10585    
## L_caudate_ComputeArea                                       0.86111    
## L_caudate_Volume                                            0.56942    
## R_caudate_ComputeArea                                       0.98901    
## R_caudate_Volume                                            0.36666    
## chr12_rs34637584_GT                                              NA    
## chr17_rs11868035_GT                                         0.67465    
## chr17_rs11012_GT                                            0.56332    
## chr17_rs393152_GT                                           0.03767 *  
## chr17_rs12185268_GT                                         0.39159    
## chr17_rs199533_GT                                           0.95729    
## Sex                                                         0.29908    
## Weight                                                      0.97547    
## Age                                                         0.01855 *  
## UPDRS_Part_I_Summary_Score_Baseline                         0.26588    
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline  0.31898    
## UPDRS_Part_III_Summary_Score_Baseline                       0.00272 ** 
## FID_IID                                                     0.37004    
## COGSTATE                                                    0.00044 ***
## COGDECLN                                                    0.87640    
## FNCDTCOG                                                    0.51870    
## COGDXCL                                                     0.30460    
## EDUCYRS                                                     0.57194    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Scale is fixed.
## 
## Correlation: Structure = exchangeable  Link = identity 
## 
## Estimated Correlation Parameters:
##       Estimate  Std.err
## alpha 7.05e-12 3.67e-12
## Number of clusters:   423   Maximum cluster size: 3
library(lme4)
#model_lmm_imaging<-glmer(PD~L_superior_parietal_gyrus_ComputeArea
 #                        +L_superior_parietal_gyrus_Volume+R_superior_parietal_gyrus_ComputeArea+R_superior_parietal_gyrus_Volume+L_putamen_ComputeArea+L_putamen_Volume+R_putamen_Volume 
  #                       +R_putamen_ShapeIndex+L_caudate_ComputeArea+L_caudate_Volume+R_caudate_ComputeArea+R_caudate_Volume+chr12_rs34637584_GT 
   #                      +chr17_rs11868035_GT+chr17_rs11012_GT+chr17_rs393152_GT+chr17_rs12185268_GT+chr17_rs199533_GT+Sex+Weight+Age+UPDRS_Part_I_Summary_Score_Baseline+UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline+UPDRS_Part_III_Summary_Score_Baseline+FID_IID+COGSTATE+COGDECLN+FNCDTCOG+COGDXCL+EDUCYRS
    #                     +(1|FID_IID),#control = glmerControl(optCtrl=list(maxfun=20000)),
     #                    data=DataMissOm,family="binomial")
#summary(model_lmm_imaging)
length(unique(DataMissOm$FID_IID))
## [1] 423
nrow(DataMissOm) 
## [1] 643

baseline analysis

ppmi_1<-ppmi[ppmi$VisitID==1,]
ppmi_1_complete<-ppmi_1[,c(1,
                           3:282, # imaging index
                           283:284,287, #demographic index
                           288,291,294,297,300,303, #genotype
                           336,348,360,384,392, #UPDRS+asessment non motor may delete 372
                           400:404, #clinical index
                           405:406)]
ppmi_1_complete$ind<-is.na(ppmi_1_complete$chr17_rs199533_GT)
ppmi_1_complete<-ppmi_1_complete[ppmi_1_complete$ind==FALSE,-303]
ppmi_MI<-ppmi_1_complete[,c(291:300)]

# Multiple Imputation
library(mi)
## Loading required package: stats4
## mi (Version 1.0, packaged: 2015-04-16 14:03:10 UTC; goodrich)
## mi  Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
## This program comes with ABSOLUTELY NO WARRANTY.
## This is free software, and you are welcome to redistribute it
## under the General Public License version 2 or later.
## Execute RShowDoc('COPYING') for details.
set.seed(1414)
mdf<-missing_data.frame(ppmi_MI)
## NOTE: The following pairs of variables appear to have the same missingness pattern.
##  Please verify whether they are in fact logically distinct variables.
##      [,1]       [,2]      
## [1,] "COGDECLN" "FNCDTCOG"
## [2,] "COGDECLN" "COGDXCL" 
## [3,] "FNCDTCOG" "COGDXCL"
summary(mdf)
##  UPDRS_Part_I_Summary_Score_Baseline
##  Min.   : 0.00                      
##  1st Qu.: 0.00                      
##  Median : 1.00                      
##  Mean   : 1.06                      
##  3rd Qu.: 2.00                      
##  Max.   :10.00                      
##  NA's   :2                          
##  UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline
##  Min.   : 0.00                                             
##  1st Qu.: 1.00                                             
##  Median : 3.00                                             
##  Mean   : 4.41                                             
##  3rd Qu.: 7.00                                             
##  Max.   :25.00                                             
##  NA's   :3                                                 
##  UPDRS_Part_III_Summary_Score_Baseline
##  Min.   : 0                           
##  1st Qu.: 3                           
##  Median :16                           
##  Mean   :15                           
##  3rd Qu.:23                           
##  Max.   :47                           
##  NA's   :2                            
##  X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Baseline
##  Min.   : 0.00                                                         
##  1st Qu.: 3.00                                                         
##  Median : 6.00                                                         
##  Mean   : 6.02                                                         
##  3rd Qu.: 8.00                                                         
##  Max.   :19.00                                                         
##  NA's   :4                                                             
##  X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline
##  Min.   : 1.00                                                                     
##  1st Qu.: 5.00                                                                     
##  Median : 5.00                                                                     
##  Mean   : 5.23                                                                     
##  3rd Qu.: 6.00                                                                     
##  Max.   :15.00                                                                     
##  NA's   :1                                                                         
##                                COGSTATE    COGDECLN   FNCDTCOG  
##  1930                              :  0   No   :374   No  :399  
##  1941                              :  0   Right:  0   Yes :  9  
##  1955                              :  0   Yes  : 34   NA's: 15  
##  Dementia (PDD)                    :  5   NA's : 15             
##  Mild Cognitive Impairment (PD-MCI): 52                         
##  Normal Cognition (PD-NC)          :350                         
##  NA's                              : 16                         
##        COGDXCL       EDUCYRS    
##  10% - 49% :  5   Min.   : 5.0  
##  50% - 89% : 57   1st Qu.:14.0  
##  90% - 100%:346   Median :16.0  
##  NA's      : 15   Mean   :16.1  
##                   3rd Qu.:18.0  
##                   Max.   :26.0  
## 
imputation<-mi(mdf)
complete<-complete(imputation) 
c4<-complete[[4]] #extract complete dataset from it from imputed datasets. 
# in this case, we randomly chose 4th. 
c4<-c4[,1:10]
ppmi_1<-cbind(ppmi_1_complete[,1:290],c4,ppmi_1_complete[,301:302]) #complete dataset 

ppmi_1_ROI<-ppmi_1[,c(1,23,24 ,28,29,33,34,38,39,143,144,148,149,282:302)] #complete dataset of regions of interest

write.csv(ppmi_1,"ppmi_complete_baseline.csv")
write.csv(ppmi_1_ROI,"ppmi_ROI_baseline.csv")

#####explore the distribution of baseline data ####
#categorical
col_n<-c(14,17:22,28:31)
#ppmi_1_ROI$APPRDX<-as.numeric(ppmi_1_ROI$APPRDX)

# frequency table
for (i in col_n){
  print(colnames(ppmi_1_ROI[i]))
  m<-table(ppmi_1_ROI[,i],ppmi_1_ROI[,33])
  print(m)
  print(fisher.test(m)$p.value)
}
## [1] "Sex"
##    
##      HC  PD
##   1  84 193
##   2  39 107
## [1] 0.499
## [1] "chr12_rs34637584_GT"
##    
##      HC  PD
##   0 123 296
##   1   0   4
## [1] 0.327
## [1] "chr17_rs11868035_GT"
##    
##      HC  PD
##   0  67 142
##   1  40 127
##   2  16  31
## [1] 0.16
## [1] "chr17_rs11012_GT"
##    
##      HC  PD
##   0  84 204
##   1  37  86
##   2   2  10
## [1] 0.716
## [1] "chr17_rs393152_GT"
##    
##      HC  PD
##   0  77 186
##   1  40  99
##   2   6  15
## [1] 1
## [1] "chr17_rs12185268_GT"
##    
##      HC  PD
##   0  80 189
##   1  39  98
##   2   4  13
## [1] 0.888
## [1] "chr17_rs199533_GT"
##    
##      HC  PD
##   0  82 193
##   1  39  96
##   2   2  11
## [1] 0.598
## [1] "COGSTATE"
##                                     
##                                       HC  PD
##   Dementia (PDD)                       0   5
##   Mild Cognitive Impairment (PD-MCI)   6  60
##   Normal Cognition (PD-NC)           117 235
## [1] 2.54e-05
## [1] "COGDECLN"
##      
##        HC  PD
##   No  120 264
##   Yes   3  36
## [1] 0.00134
## [1] "FNCDTCOG"
##      
##        HC  PD
##   No  123 291
##   Yes   0   9
## [1] 0.0643
## [1] "COGDXCL"
##             
##               HC  PD
##   10% - 49%    0   5
##   50% - 89%    9  59
##   90% - 100% 114 236
## [1] 0.00118
for (i in col_n){
  print(colnames(ppmi_1_ROI[i]))
  m<-table(ppmi_1_ROI[,i],ppmi_1_ROI[,34])
  print(m)
  print(fisher.test(m)$p.value)
}
## [1] "Sex"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   1            0              84                 170    23
##   2            0              39                  93    14
## [1] 0.711
## [1] "chr12_rs34637584_GT"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   0            0             123                 259    37
##   1            0               0                   4     0
## [1] 0.523
## [1] "chr17_rs11868035_GT"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   0            0              67                 127    15
##   1            0              40                 107    20
##   2            0              16                  29     2
## [1] 0.189
## [1] "chr17_rs11012_GT"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   0            0              84                 176    28
##   1            0              37                  78     8
##   2            0               2                   9     1
## [1] 0.733
## [1] "chr17_rs393152_GT"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   0            0              77                 160    26
##   1            0              40                  89    10
##   2            0               6                  14     1
## [1] 0.905
## [1] "chr17_rs12185268_GT"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   0            0              80                 163    26
##   1            0              39                  88    10
##   2            0               4                  12     1
## [1] 0.906
## [1] "chr17_rs199533_GT"
##    
##      psychiatric Healthy Control Parkinson's disease SWEDD
##   0            0              82                 167    26
##   1            0              39                  86    10
##   2            0               2                  10     1
## [1] 0.779
## [1] "COGSTATE"
##                                     
##                                       psychiatric Healthy Control
##   Dementia (PDD)                                0               0
##   Mild Cognitive Impairment (PD-MCI)            0               6
##   Normal Cognition (PD-NC)                      0             117
##                                     
##                                      Parkinson's disease SWEDD
##   Dementia (PDD)                                       5     0
##   Mild Cognitive Impairment (PD-MCI)                  47    13
##   Normal Cognition (PD-NC)                           211    24
## [1] 1.18e-05
## [1] "COGDECLN"
##      
##        psychiatric Healthy Control Parkinson's disease SWEDD
##   No             0             120                 233    31
##   Yes            0               3                  30     6
## [1] 0.00184
## [1] "FNCDTCOG"
##      
##        psychiatric Healthy Control Parkinson's disease SWEDD
##   No             0             123                 257    34
##   Yes            0               0                   6     3
## [1] 0.0142
## [1] "COGDXCL"
##             
##               psychiatric Healthy Control Parkinson's disease SWEDD
##   10% - 49%             0               0                   5     0
##   50% - 89%             0               9                  50     9
##   90% - 100%            0             114                 208    28
## [1] 0.00413
#continuous
#normality test
col_n<-c(2:13,15,16,23:27,32)
aa<-matrix(NA,20,1)
k<-1
for(i in col_n){
  aa[k,1]<-shapiro.test(ppmi_1_ROI[,i])$p.value
  k<-k+1
}
k<-1
#for(i in col_n){
# x<-ppmi_1_ROI[ppmi_1_ROI$RECRUITMENT_CAT=="HC",i] 
#  y<-ppmi_1_ROI[ppmi_1_ROI$RECRUITMENT_CAT=="PD",i] 
#  aa[k,2]<-t.test(x,y)$p.value
#  k<-k+1
#}

aa<-as.data.frame(aa)
rownames(aa)<-colnames(ppmi_1_ROI)[col_n]
colnames(aa)<-c("normality-test (>0.1 normal)")
write.csv(aa,"continuous_descriptive.csv")

model-based analysis

#logistic regression
for(i in c(2:13,15,16,23:27,32)){
  ppmi_1_ROI[,i]<-scale(ppmi_1_ROI[,i])
}
ppmi_1_ROI<-as.data.frame(ppmi_1_ROI)
levels(ppmi_1_ROI$RECRUITMENT_CAT)<-c(0,1)
ppmi_1_ROI$RECRUITMENT_CAT<-as.numeric(ppmi_1_ROI$RECRUITMENT_CAT)
ppmi_1_ROI$RECRUITMENT_CAT<-ppmi_1_ROI$RECRUITMENT_CAT-1
logistic_ROI<-glm(RECRUITMENT_CAT~.,data=ppmi_1_ROI[,-c(1,34)],maxit=50,family="binomial")
library(MASS)
stepp<-stepAIC(logistic_ROI,trace=FALSE) #stepwise logistic regression
summary(logistic_ROI)
## 
## Call:
## glm(formula = RECRUITMENT_CAT ~ ., family = "binomial", data = ppmi_1_ROI[, 
##     -c(1, 34)], maxit = 50)
## 
## Deviance Residuals: 
##       Min         1Q     Median         3Q        Max  
## -6.95e-06  -2.10e-08   2.10e-08   2.10e-08   2.01e-05  
## 
## Coefficients:
##                                                                                     Estimate
## (Intercept)                                                                        -2.60e+02
## L_caudate_ComputeArea                                                               4.40e+01
## L_caudate_Volume                                                                    3.36e+01
## R_caudate_ComputeArea                                                               1.38e+01
## R_caudate_Volume                                                                   -7.29e+01
## L_putamen_ComputeArea                                                               1.06e+02
## L_putamen_Volume                                                                   -9.39e+01
## R_putamen_ComputeArea                                                               5.60e+01
## R_putamen_Volume                                                                   -5.98e+01
## L_superior_parietal_gyrus_ComputeArea                                               1.49e+02
## L_superior_parietal_gyrus_Volume                                                   -1.96e+02
## R_superior_parietal_gyrus_ComputeArea                                              -3.50e+01
## R_superior_parietal_gyrus_Volume                                                    7.10e+01
## Sex                                                                                 2.96e+01
## Weight                                                                              5.44e+00
## Age                                                                                -5.12e+01
## chr12_rs34637584_GT                                                                -4.31e+02
## chr17_rs11868035_GT                                                                -4.24e+01
## chr17_rs11012_GT                                                                    6.88e+00
## chr17_rs393152_GT                                                                  -4.84e+01
## chr17_rs12185268_GT                                                                -1.43e+01
## chr17_rs199533_GT                                                                  -3.41e+01
## UPDRS_Part_I_Summary_Score_Baseline                                                -2.50e+01
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                          1.99e+02
## UPDRS_Part_III_Summary_Score_Baseline                                               3.71e+02
## X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Baseline             -1.05e+01
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline -1.79e+01
## COGSTATEMild Cognitive Impairment (PD-MCI)                                          3.16e+02
## COGSTATENormal Cognition (PD-NC)                                                    2.70e+02
## COGDECLNYes                                                                         7.25e+01
## FNCDTCOGYes                                                                        -3.18e+02
## COGDXCL50% - 89%                                                                    2.59e+02
## COGDXCL90% - 100%                                                                   4.09e+02
## EDUCYRS                                                                             1.43e+01
##                                                                                    Std. Error
## (Intercept)                                                                          1.89e+07
## L_caudate_ComputeArea                                                                1.39e+07
## L_caudate_Volume                                                                     1.33e+07
## R_caudate_ComputeArea                                                                1.47e+07
## R_caudate_Volume                                                                     1.62e+07
## L_putamen_ComputeArea                                                                8.55e+06
## L_putamen_Volume                                                                     8.04e+06
## R_putamen_ComputeArea                                                                1.07e+07
## R_putamen_Volume                                                                     1.10e+07
## L_superior_parietal_gyrus_ComputeArea                                                1.56e+07
## L_superior_parietal_gyrus_Volume                                                     1.74e+07
## R_superior_parietal_gyrus_ComputeArea                                                1.34e+07
## R_superior_parietal_gyrus_Volume                                                     1.36e+07
## Sex                                                                                  6.03e+06
## Weight                                                                               2.48e+06
## Age                                                                                  2.60e+06
## chr12_rs34637584_GT                                                                  3.42e+07
## chr17_rs11868035_GT                                                                  3.32e+06
## chr17_rs11012_GT                                                                     8.23e+06
## chr17_rs393152_GT                                                                    5.98e+06
## chr17_rs12185268_GT                                                                  8.23e+06
## chr17_rs199533_GT                                                                    7.76e+06
## UPDRS_Part_I_Summary_Score_Baseline                                                  2.90e+06
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                           4.19e+06
## UPDRS_Part_III_Summary_Score_Baseline                                                3.77e+06
## X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Baseline               1.66e+06
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline   2.86e+06
## COGSTATEMild Cognitive Impairment (PD-MCI)                                           2.71e+07
## COGSTATENormal Cognition (PD-NC)                                                     2.75e+07
## COGDECLNYes                                                                          1.39e+07
## FNCDTCOGYes                                                                          1.73e+07
## COGDXCL50% - 89%                                                                     2.49e+07
## COGDXCL90% - 100%                                                                    2.46e+07
## EDUCYRS                                                                              2.40e+06
##                                                                                    z value
## (Intercept)                                                                              0
## L_caudate_ComputeArea                                                                    0
## L_caudate_Volume                                                                         0
## R_caudate_ComputeArea                                                                    0
## R_caudate_Volume                                                                         0
## L_putamen_ComputeArea                                                                    0
## L_putamen_Volume                                                                         0
## R_putamen_ComputeArea                                                                    0
## R_putamen_Volume                                                                         0
## L_superior_parietal_gyrus_ComputeArea                                                    0
## L_superior_parietal_gyrus_Volume                                                         0
## R_superior_parietal_gyrus_ComputeArea                                                    0
## R_superior_parietal_gyrus_Volume                                                         0
## Sex                                                                                      0
## Weight                                                                                   0
## Age                                                                                      0
## chr12_rs34637584_GT                                                                      0
## chr17_rs11868035_GT                                                                      0
## chr17_rs11012_GT                                                                         0
## chr17_rs393152_GT                                                                        0
## chr17_rs12185268_GT                                                                      0
## chr17_rs199533_GT                                                                        0
## UPDRS_Part_I_Summary_Score_Baseline                                                      0
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                               0
## UPDRS_Part_III_Summary_Score_Baseline                                                    0
## X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Baseline                   0
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline       0
## COGSTATEMild Cognitive Impairment (PD-MCI)                                               0
## COGSTATENormal Cognition (PD-NC)                                                         0
## COGDECLNYes                                                                              0
## FNCDTCOGYes                                                                              0
## COGDXCL50% - 89%                                                                         0
## COGDXCL90% - 100%                                                                        0
## EDUCYRS                                                                                  0
##                                                                                    Pr(>|z|)
## (Intercept)                                                                               1
## L_caudate_ComputeArea                                                                     1
## L_caudate_Volume                                                                          1
## R_caudate_ComputeArea                                                                     1
## R_caudate_Volume                                                                          1
## L_putamen_ComputeArea                                                                     1
## L_putamen_Volume                                                                          1
## R_putamen_ComputeArea                                                                     1
## R_putamen_Volume                                                                          1
## L_superior_parietal_gyrus_ComputeArea                                                     1
## L_superior_parietal_gyrus_Volume                                                          1
## R_superior_parietal_gyrus_ComputeArea                                                     1
## R_superior_parietal_gyrus_Volume                                                          1
## Sex                                                                                       1
## Weight                                                                                    1
## Age                                                                                       1
## chr12_rs34637584_GT                                                                       1
## chr17_rs11868035_GT                                                                       1
## chr17_rs11012_GT                                                                          1
## chr17_rs393152_GT                                                                         1
## chr17_rs12185268_GT                                                                       1
## chr17_rs199533_GT                                                                         1
## UPDRS_Part_I_Summary_Score_Baseline                                                       1
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                                1
## UPDRS_Part_III_Summary_Score_Baseline                                                     1
## X_Assessment_Non.Motor_Epworth_Sleepiness_Scale_Summary_Score_Baseline                    1
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline        1
## COGSTATEMild Cognitive Impairment (PD-MCI)                                                1
## COGSTATENormal Cognition (PD-NC)                                                          1
## COGDECLNYes                                                                               1
## FNCDTCOGYes                                                                               1
## COGDXCL50% - 89%                                                                          1
## COGDXCL90% - 100%                                                                         1
## EDUCYRS                                                                                   1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 5.1001e+02  on 422  degrees of freedom
## Residual deviance: 5.0390e-10  on 389  degrees of freedom
## AIC: 68
## 
## Number of Fisher Scoring iterations: 46
summary(stepp)
## 
## Call:
## glm(formula = RECRUITMENT_CAT ~ L_caudate_ComputeArea + R_caudate_ComputeArea + 
##     R_caudate_Volume + R_putamen_ComputeArea + L_superior_parietal_gyrus_ComputeArea + 
##     L_superior_parietal_gyrus_Volume + R_superior_parietal_gyrus_ComputeArea + 
##     R_superior_parietal_gyrus_Volume + Age + chr17_rs393152_GT + 
##     UPDRS_Part_I_Summary_Score_Baseline + UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline + 
##     UPDRS_Part_III_Summary_Score_Baseline + X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline + 
##     EDUCYRS, family = "binomial", data = ppmi_1_ROI[, -c(1, 34)], 
##     maxit = 50)
## 
## Deviance Residuals: 
##       Min         1Q     Median         3Q        Max  
## -2.13e-05  -2.10e-08   2.10e-08   2.10e-08   2.43e-05  
## 
## Coefficients:
##                                                                                    Estimate
## (Intercept)                                                                            4717
## L_caudate_ComputeArea                                                                   719
## R_caudate_ComputeArea                                                                  2747
## R_caudate_Volume                                                                      -2974
## R_putamen_ComputeArea                                                                   284
## L_superior_parietal_gyrus_ComputeArea                                                  1332
## L_superior_parietal_gyrus_Volume                                                      -1632
## R_superior_parietal_gyrus_ComputeArea                                                  1932
## R_superior_parietal_gyrus_Volume                                                      -2284
## Age                                                                                    -912
## chr17_rs393152_GT                                                                      -539
## UPDRS_Part_I_Summary_Score_Baseline                                                    -312
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                             2269
## UPDRS_Part_III_Summary_Score_Baseline                                                  4878
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline     -473
## EDUCYRS                                                                                 368
##                                                                                    Std. Error
## (Intercept)                                                                           1809724
## L_caudate_ComputeArea                                                                  290702
## R_caudate_ComputeArea                                                                 1152221
## R_caudate_Volume                                                                      1224145
## R_putamen_ComputeArea                                                                  128396
## L_superior_parietal_gyrus_ComputeArea                                                  691206
## L_superior_parietal_gyrus_Volume                                                       811154
## R_superior_parietal_gyrus_ComputeArea                                                  822670
## R_superior_parietal_gyrus_Volume                                                       989893
## Age                                                                                    352578
## chr17_rs393152_GT                                                                      235286
## UPDRS_Part_I_Summary_Score_Baseline                                                    211657
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                             883129
## UPDRS_Part_III_Summary_Score_Baseline                                                 1873873
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline     195285
## EDUCYRS                                                                                179889
##                                                                                    z value
## (Intercept)                                                                              0
## L_caudate_ComputeArea                                                                    0
## R_caudate_ComputeArea                                                                    0
## R_caudate_Volume                                                                         0
## R_putamen_ComputeArea                                                                    0
## L_superior_parietal_gyrus_ComputeArea                                                    0
## L_superior_parietal_gyrus_Volume                                                         0
## R_superior_parietal_gyrus_ComputeArea                                                    0
## R_superior_parietal_gyrus_Volume                                                         0
## Age                                                                                      0
## chr17_rs393152_GT                                                                        0
## UPDRS_Part_I_Summary_Score_Baseline                                                      0
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                               0
## UPDRS_Part_III_Summary_Score_Baseline                                                    0
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline       0
## EDUCYRS                                                                                  0
##                                                                                    Pr(>|z|)
## (Intercept)                                                                               1
## L_caudate_ComputeArea                                                                     1
## R_caudate_ComputeArea                                                                     1
## R_caudate_Volume                                                                          1
## R_putamen_ComputeArea                                                                     1
## L_superior_parietal_gyrus_ComputeArea                                                     1
## L_superior_parietal_gyrus_Volume                                                          1
## R_superior_parietal_gyrus_ComputeArea                                                     1
## R_superior_parietal_gyrus_Volume                                                          1
## Age                                                                                       1
## chr17_rs393152_GT                                                                         1
## UPDRS_Part_I_Summary_Score_Baseline                                                       1
## UPDRS_Part_II_Patient_Questionnaire_Summary_Score_Baseline                                1
## UPDRS_Part_III_Summary_Score_Baseline                                                     1
## X_Assessment_Non.Motor_Geriatric_Depression_Scale_GDS_Short_Summary_Score_Baseline        1
## EDUCYRS                                                                                   1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 5.1001e+02  on 422  degrees of freedom
## Residual deviance: 3.9038e-09  on 407  degrees of freedom
## AIC: 32
## 
## Number of Fisher Scoring iterations: 38
#logistic_complete<-glm(RECRUITMENT_CAT~.,data=ppmi_1[,-c(1,302)],maxit=50,family="binomial")
#stepp<-stepAIC(logistic_complete,trace=FALSE) #stepwise model selection of ROI data
#summary(stepp)


#ppmi_1 complete
ppmi_1_PD1<-ppmi_1[ppmi_1$APPRDX!="psychiatric",]
ppmi_1_PD1<-ppmi_1[ppmi_1$APPRDX!="SWEDD",]
ppmi_1_PD1<-ppmi_1_PD1[,-c(1,302)]
ppmi_1_PD2<-ppmi_1[ppmi_1$APPRDX!="psychiatric",]
ppmi_1_PD2<-ppmi_1[,-c(1,302)]

ppmi_1_PD1$PD1<-ifelse(ppmi_1_PD1$RECRUITMENT_CAT=="HC",1,0)
ppmi_1_PD1<-ppmi_1_PD1[,-300]
ppmi_1_PD1$PD1<-as.factor(ppmi_1_PD1$PD1)

Balance cases

#PD1=PD PD2=PD+SWEDD
set.seed(623)

library(unbalanced)
## Loading required package: mlr
## Loading required package: BBmisc
## Loading required package: ggplot2
## Loading required package: ParamHelpers
## Loading required package: stringi
## Loading required package: foreach
## Loading required package: doParallel
## Loading required package: iterators
## Loading required package: parallel
n<-ncol(ppmi_1_PD1)
output<-ppmi_1_PD1$PD1
input<-ppmi_1_PD1[ ,-n]

#balance the dataset
data<-ubBalance(X= input, Y=output,type="ubSMOTE", verbose=TRUE)
## Proportion of positives after ubSMOTE : 42.9 % of 861 observations
balancedData<-cbind(data$X,data$Y)
ppmi_1_PD1_balanced<-balancedData
colnames(ppmi_1_PD1_balanced)<-colnames(ppmi_1_PD1)


ppmi_1_PD2$PD2<-ifelse(ppmi_1_PD2$RECRUITMENT_CAT=="HC",1,0)
ppmi_1_PD2<-ppmi_1_PD2[,-300]
ppmi_1_PD2$PD2<-as.factor(ppmi_1_PD2$PD2)
#balance cases
set.seed(623)
require(unbalanced)
n<-ncol(ppmi_1_PD2)
output<-ppmi_1_PD2$PD2
input<-ppmi_1_PD2[ ,-n]

#balance the dataset
data<-ubBalance(X= input, Y=output,type="ubSMOTE", verbose=TRUE)
## Proportion of positives after ubSMOTE : 42.9 % of 861 observations
balancedData<-cbind(data$X,data$Y)
ppmi_1_PD2_balanced<-balancedData
colnames(ppmi_1_PD2_balanced)<-colnames(ppmi_1_PD2)

#numerize the 4 datasets
for(i in 295:298){
  ppmi_1_PD1[,i]<-as.numeric(ppmi_1_PD1[,i])
}
for(i in 295:298){
  ppmi_1_PD2[,i]<-as.numeric(ppmi_1_PD2[,i])
}
for(i in 295:298){
  ppmi_1_PD1_balanced[,i]<-as.numeric(ppmi_1_PD1_balanced[,i])
}
for(i in 295:298){
  ppmi_1_PD2_balanced[,i]<-as.numeric(ppmi_1_PD2_balanced[,i])
}

write.csv(ppmi_1_PD1,"PD1_un.csv")
write.csv(ppmi_1_PD2,"PD2_un.csv")
write.csv(ppmi_1_PD1_balanced,"PD1_b.csv")
write.csv(ppmi_1_PD2_balanced,"PD2_b.csv")
### Prediction functions ####
# cv 5 functions
library(crossval)
## 
## Attaching package: 'crossval'
## The following object is masked from 'package:mlr':
## 
##     crossval
#adaboost
library(ada)
## Loading required package: rpart
library(rpart)
my.ada <- function (train.x, train.y, test.x, test.y, negative, formula){
  ada.fit <- ada(train.x, train.y)
  predict.y <- predict(ada.fit, test.x)
  #count TP,NP..
  out <- confusionMatrix(test.y, predict.y, negative = negative)
  return (out)
}


# svm
library(e1071)
## 
## Attaching package: 'e1071'
## The following object is masked from 'package:mlr':
## 
##     impute
my.svm <- function (train.x, train.y, test.x, test.y, negative, formula){
  svm.fit <- svm(train.x, train.y)
  predict.y <- predict(svm.fit, test.x)
  #count TP,NP..
  out <- confusionMatrix(test.y, predict.y, negative = negative)
  return (out)
}
# naive bayesian
my.nb <- function (train.x, train.y, test.x, test.y, negative, formula){
  nb.fit <- naiveBayes(train.x, train.y)
  predict.y <- predict(nb.fit, test.x)
  #count TP,NP..
  out <- confusionMatrix(test.y, predict.y, negative = negative)
  return (out)
}
# decision trees

library(rpart)
my.detree <- function (train.x, train.y, test.x, test.y, negative, formula){
  train.matrix<-cbind(train.x,train.y)
  detree.fit <- rpart(train.y~.,method="class",data=train.matrix)
  predict.y <- predict(detree.fit, test.x)
  out <- confusionMatrix(test.y, predict.y, negative = negative)
  return (out)
}
##k-Nearest Neighbor Classiï¬cation

library("class")
my.knn <- function (train.x, train.y, test.x, test.y, negative, formula){
  train.matrix<-cbind(train.x,train.y)
  test.matrix<-cbind(test.x,test.y)
  predict.y <- knn(train=train.matrix,test=test.matrix,cl=train.y,k=2)
  out <- confusionMatrix(test.y, predict.y, negative = negative)
  return (out)
}
## Kmeans
my.kmeans <- function (train.x, train.y, test.x, test.y, negative, formula){
  train.matrix<-cbind(train.x,train.y)
  test.matrix<-cbind(test.x,test.y)
  kmeans.fit <- kmeans(train.x,2)
  predict.y <- kmeans.fit$cluster-1
  out <- confusionMatrix(test.y,predict.y, negative = negative)
  return (out)
}

function dealt with complete dataset

classfi<-function(a=my.ada){
  a1<-matrix(NA,4,4)
  a2<-matrix(NA,4,6)
  #PD1 unbalanced
  X <- ppmi_1_PD1[, 1:299]
  Y <- ppmi_1_PD1[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  a1[1,]<-cv.out$stat
  a2[1,]<-out
  
  
  
  #PD2 unbalanced
  X <- ppmi_1_PD2[, 1:299]
  Y <- ppmi_1_PD2[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  
  a1[2,]<-cv.out$stat
  a2[2,]<-out
  
  #PD1 balanced
  X <- ppmi_1_PD1_balanced[, 1:299]
  Y <- ppmi_1_PD1_balanced[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  
  a1[3,]<-cv.out$stat
  a2[3,]<-out
  
  #PD2 balanced
  X <- ppmi_1_PD2_balanced[, 1:299]
  Y <- ppmi_1_PD2_balanced[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  a1[4,]<-cv.out$stat
  a2[4,]<-out
  classification<-as.data.frame(cbind(a1,a2))
  classification$Group<-c("PD1_un","PD2_un","PD1_b","PD2_b")
  write.csv(classification,"classification.csv")
  print(classification)
}

Classification result

# adaboost
classfi()
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##    V1   V2   V3  V4    V5    V6    V7    V8    V9   V10  Group
## 1 0.8 23.0 51.8 1.6 0.969 0.935 0.985 0.966 0.970  6.84 PD1_un
## 2 1.2 22.6 58.8 2.0 0.962 0.919 0.980 0.950 0.967  6.32 PD2_un
## 3 0.2 73.4 98.2 0.4 0.997 0.995 0.998 0.997 0.996 11.41  PD1_b
## 4 1.8 72.6 96.6 1.2 0.983 0.984 0.982 0.976 0.988  8.09  PD2_b
# detree
classfi(a=my.detree)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      V1    V2   V3  V4    V5    V6      V7    V8    V9   V10  Group
## 1  93.4  44.2 11.8 5.0 0.363 0.898 0.11217 0.321 0.702  0.11 PD1_un
## 2 120.0  49.2  0.0 0.0 0.291 1.000 0.00000 0.291   NaN   NaN PD2_un
## 3 176.0 145.4 20.8 2.2 0.483 0.985 0.10569 0.452 0.904  2.06  PD1_b
## 4 196.4 146.4  0.4 1.2 0.426 0.992 0.00203 0.427 0.250 -1.39  PD2_b
#naive bayes
classfi(a=my.nb)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##     V1   V2   V3   V4    V5    V6    V7    V8    V9   V10  Group
## 1 11.2  8.6 41.4 16.0 0.648 0.350 0.787 0.434 0.721 0.687 PD1_un
## 2 13.4 11.4 46.6 13.2 0.686 0.463 0.777 0.460 0.779 1.100 PD2_un
## 3 55.2 64.8 43.2  9.0 0.627 0.878 0.439 0.540 0.828 1.729  PD1_b
## 4 55.2 65.4 43.2  8.4 0.631 0.886 0.439 0.542 0.837 1.807  PD2_b
#svm
classfi(a=my.svm)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##    V1   V2   V3   V4    V5     V6    V7    V8    V9  V10  Group
## 1 0.4  6.8 52.2 17.8 0.764 0.2764 0.992 0.944 0.746 3.91 PD1_un
## 2 0.6  2.0 59.4 22.6 0.726 0.0813 0.990 0.769 0.724 2.17 PD2_un
## 3 2.0 69.6 96.4  4.2 0.964 0.9431 0.980 0.972 0.958 6.68  PD1_b
## 4 2.6 68.4 95.8  5.4 0.954 0.9268 0.974 0.963 0.947 6.15  PD2_b
# knn
classfi(a=my.knn)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##     V1   V2   V3   V4    V5    V6    V7    V8    V9    V10  Group
## 1 15.2  7.6 37.4 17.0 0.583 0.309 0.711 0.333 0.688 0.0953 PD1_un
## 2 17.2  7.2 42.8 17.4 0.591 0.293 0.713 0.295 0.711 0.0292 PD2_un
## 3 17.8 55.2 80.6 18.6 0.789 0.748 0.819 0.756 0.812 2.5981  PD1_b
## 4 20.4 56.2 78.0 17.6 0.779 0.762 0.793 0.734 0.816 2.5022  PD2_b
# kmeans
classfi(a=my.kmeans)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      V1    V2  V3    V4    V5    V6    V7    V8    V9     V10  Group
## 1  87.6  38.4 124  58.4 0.527 0.397 0.587 0.305 0.681 -0.0685 PD1_un
## 2 114.2  44.6 127  52.6 0.507 0.459 0.527 0.281 0.707 -0.0587 PD2_un
## 3 163.6 126.0 232 167.6 0.519 0.429 0.586 0.435 0.580  0.0623  PD1_b
## 4 165.4 124.2 230 169.4 0.514 0.423 0.581 0.429 0.576  0.0185  PD2_b

function dealt with dataset without UPDRS (and clinical features)

classfi1<-function(a=my.ada){
  a1<-matrix(NA,4,4)
  a2<-matrix(NA,4,6)
  #PD1 unbalanced
  X <- ppmi_1_PD1[, 1:289]
  Y <- ppmi_1_PD1[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  a1[1,]<-cv.out$stat
  a2[1,]<-out
  
  
  
  #PD2 unbalanced
  X <- ppmi_1_PD2[, 1:289]
  Y <- ppmi_1_PD2[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  
  a1[2,]<-cv.out$stat
  a2[2,]<-out
  
  #PD1 balanced
  X <- ppmi_1_PD1_balanced[, 1:289]
  Y <- ppmi_1_PD1_balanced[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  
  a1[3,]<-cv.out$stat
  a2[3,]<-out
  
  #PD2 balanced
  X <- ppmi_1_PD2_balanced[, 1:289]
  Y <- ppmi_1_PD2_balanced[,300] 
  form <- "train.y~." 
  neg <- 0
  set.seed(714)
  cv.out <- crossval(a, X, Y, K = 5, B = 1, negative = neg, formula = form)
  out <- diagnosticErrors(cv.out$stat) 
  a1[4,]<-cv.out$stat
  a2[4,]<-out
  classification<-cbind(a1,a2)
  write.csv(classification,"classification2.csv")
  print(classification)
}
#adaboost
classfi1(a=my.ada)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      [,1] [,2] [,3] [,4]  [,5]   [,6]  [,7]  [,8]  [,9] [,10]
## [1,]  4.0  4.0 48.6 20.6 0.681 0.1626 0.924 0.500 0.702 0.858
## [2,]  4.2  2.0 55.8 22.6 0.683 0.0813 0.930 0.323 0.712 0.162
## [3,]  2.8 58.0 95.6 15.8 0.892 0.7859 0.972 0.954 0.858 4.831
## [4,]  4.6 55.8 93.8 18.0 0.869 0.7561 0.953 0.924 0.839 4.147
#detree
classfi1(a=my.detree)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      [,1]  [,2] [,3] [,4]  [,5]  [,6]   [,7]  [,8]  [,9]   [,10]
## [1,]  100  47.4  5.0  1.8 0.339 0.963 0.0475 0.321 0.735  0.2731
## [2,]  115  48.2  5.0  1.0 0.314 0.980 0.0417 0.295 0.833  0.7399
## [3,]  187 139.8  9.8  7.8 0.434 0.947 0.0498 0.428 0.557 -0.0626
## [4,]  189 139.6  7.4  8.0 0.427 0.946 0.0376 0.424 0.481 -0.3830
#naive bayes
classfi1(a=my.nb)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      [,1] [,2] [,3] [,4]  [,5]  [,6]  [,7]  [,8]  [,9] [,10]
## [1,] 13.0  7.8 39.6 16.8 0.614 0.317 0.753 0.375 0.702 0.347
## [2,] 16.6  8.8 43.4 15.8 0.617 0.358 0.723 0.346 0.733 0.376
## [3,] 72.4 64.2 26.0  9.6 0.524 0.870 0.264 0.470 0.730 0.876
## [4,] 70.6 64.6 27.8  9.2 0.537 0.875 0.283 0.478 0.751 1.017
# svm
classfi1(a=my.svm)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      [,1] [,2] [,3] [,4]  [,5]    [,6]  [,7]  [,8]  [,9] [,10]
## [1,]  0.2  0.4 52.4 24.2 0.684 0.01626 0.996 0.667 0.684  1.47
## [2,]  0.4  0.2 59.6 24.4 0.707 0.00813 0.993 0.333 0.710  0.20
## [3,]  4.8 53.0 93.6 20.8 0.851 0.71816 0.951 0.917 0.818  3.91
## [4,]  4.2 50.4 94.2 23.4 0.840 0.68293 0.957 0.923 0.801  3.88
# knn
classfi1(a=my.knn)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##      [,1] [,2] [,3] [,4]  [,5]  [,6]  [,7]  [,8]  [,9]  [,10]
## [1,] 15.2  7.6 37.4 17.0 0.583 0.309 0.711 0.333 0.688 0.0953
## [2,] 17.2  7.2 42.8 17.4 0.591 0.293 0.713 0.295 0.711 0.0292
## [3,] 17.8 55.2 80.6 18.6 0.789 0.748 0.819 0.756 0.812 2.5981
## [4,] 20.4 56.2 78.0 17.6 0.779 0.762 0.793 0.734 0.816 2.5022
# kmeans
classfi1(a=my.kmeans)
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
## Number of folds: 5 
## Total number of CV fits: 5 
## 
## Round # 1 of 1 
## CV Fit # 1 of 5 
## CV Fit # 2 of 5 
## CV Fit # 3 of 5 
## CV Fit # 4 of 5 
## CV Fit # 5 of 5 
##       [,1]  [,2] [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9]   [,10]
## [1,]  87.6  38.4  124  58.4 0.527 0.397 0.587 0.305 0.681 -0.0685
## [2,] 114.2  44.6  127  52.6 0.507 0.459 0.527 0.281 0.707 -0.0587
## [3,] 163.6 126.0  232 167.6 0.519 0.429 0.586 0.435 0.580  0.0623
## [4,] 165.4 124.2  230 169.4 0.514 0.423 0.581 0.429 0.576  0.0185

adaboost scores and results

# Varplot, table S2 and table S3
require(ada)
#unbalanced PD1
set.seed(729) 
c1<-ada(PD1~.,data=ppmi_1_PD1)

n_c<-ncol(ppmi_1_PD1)-1
PD1_score<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD1","unBalanced")
write.csv(data_top30,"top30.csv")

#unbalanced PD2
set.seed(729) 
c1<-ada(PD2~.,data=ppmi_1_PD2)

n_c<-ncol(ppmi_1_PD2)-1
PD2_score<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD2","unBalanced")
write.csv(data_top30,"top30.csv")

#balanced PD1
set.seed(729) 
c1<-ada(PD1~.,data=ppmi_1_PD1_balanced)

n_c<-ncol(ppmi_1_PD1_balanced)-1
PD1_score_b<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD1","Balanced")
write.csv(data_top30,"top30.csv")


#balanced PD2
set.seed(729) 
c1<-ada(PD2~.,data=ppmi_1_PD2_balanced)

n_c<-ncol(ppmi_1_PD2_balanced)-1
PD2_score_b<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD2","Balanced")
write.csv(data_top30,"top30.csv")


write.csv(PD1_score,"trial1.csv")
write.csv(PD2_score,"trial2.csv")
write.csv(PD1_score_b,"trial3.csv")
write.csv(PD2_score_b,"trial4.csv")
########

without UPDRS

#unbalanced PD1
set.seed(729) 
c1<-ada(PD1~.,data=ppmi_1_PD1[,-c(290:294)])

n_c<-ncol(ppmi_1_PD1[,-c(290:294)])-1
PD1_score_noUPDRS<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD1","unBalanced")
write.csv(data_top30,"top30.csv")

#unbalanced PD2
set.seed(729) 
c1<-ada(PD2~.,data=ppmi_1_PD2[,-c(290:294)])

n_c<-ncol(ppmi_1_PD2[,-c(290:294)])-1
PD2_score_noUPDRS<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD2","unBalanced")
write.csv(data_top30,"top30.csv")


#balanced PD1
set.seed(729) 
c1<-ada(PD1~.,data=ppmi_1_PD1_balanced[,-c(290:294)])

n_c<-ncol(ppmi_1_PD1_balanced[,-c(290:294)])-1
PD1_score_b_noUPDRS<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD1","Balanced")
write.csv(data_top30,"top30.csv")

#balanced PD2
set.seed(729) 
c1<-ada(PD2~.,data=ppmi_1_PD2_balanced[,-c(290:294)])

n_c<-ncol(ppmi_1_PD2_balanced[,-c(290:294)])-1
PD2_score_b_noUPDRS<-varplot(c1,type="scores",max.var.show=n_c)

top30<-varplot(c1,type="scores")

data_top30<-cbind(names(top30),"PD2","Balanced")
write.csv(data_top30,"top30.csv")

write.csv(PD1_score_noUPDRS,"trial5.csv")
write.csv(PD2_score_noUPDRS,"trial6.csv")
write.csv(PD1_score_b_noUPDRS,"trial7.csv")
write.csv(PD2_score_b_noUPDRS,"trial8.csv")

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.